Molecular dynamics simulations and mechanism of organic reactions: Non-TST behaviors

Advances in Physical Organic Chemistry

Volumn 44, Issue C, 2010, Pages 173-222

  Yamataka, Hiroshi ^a  

^a RIKKYO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85023077404     PISSN: 00653160     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3160(08)44004-2     Document Type: Review

References (146)

1. B.K. Carpenter J Am Chem Soc 107 1985 5730 5732
2. J.E. Baldwin K.D. Belfield J Am Chem Soc 110 1988 296 297
3. F.-G. Klarner R. Drewes D. Hasselman J Am Chem Soc 110 1988 297 298
4. B.K. Carpenter J Am Chem Soc 117 1995 6336 6344
5. B.K. Carpenter J Am Chem Soc 118 1996 10329 10330
6. B.A. Lyons J. Pfeifer T.H. Peterson B.K. Carpenter J Am Chem Soc 115 1993 2427 2437
7. M.B. Reys B.K. Carpenters J Am Chem Soc 120 1998 1641 1642
8. M.B. Reyes B.K. Carpenter J Am Chem Soc 122 2000 10163 10176
9. C. Doubleday C.P. Suhrada K.N. Houk J Am Chem Soc 128 2006 90 94
10. S. Pedersen J.L. Herek A.H. Zewail Science 266 1994 1359 1364
11. C. Doubleday Jr. J Phys Chem 100 1996 3520 3526
12. C. Doubleday Jr. K. Bolton G.H. Peslherbe W.L. Hase J Am Chem Soc 118 1996 9922 9931
13. C. Doubleday K. Bolton W.L. Hase J Am Chem Soc 119 1997 5251 5252
14. C. Doubleday Jr. K. Bolton W.L. Hase J Phys Chem A 102 1998 3648 3658
15. D.A. Hrovat S. Fang W.T. Borden B.K. Carpenter J Am Chem Soc 119 1997 5253 5254
16. K. Bolton W.L. Hase C. Doubleday Jr. J Phys Chem B 103 1999 3691 3698
17. C. Doubleday M. Nendel K.N. Houk D. Thweatt M. Page J Am Chem Soc 121 1999 4720 4721
18. C. Doubleday J Phys Chem A 105 2001 6333 6341
19. C. Doubleday G. Li W.L. Hase Phys Chem Chem Phys 4 2002 304 312
20. J.E. Baldwin K.A. Villarica D.I. Freedberg F.A.L. Anet J Am Chem Soc 116 1994 10845 10846
21. K.N. Houk M. Nendel O. Wiest J.W. Storer J Am Chem Soc 119 1997 10545 10546
22. M. Nendel D. Sperling O. Wiest K.N. Houk J Org Chem 65 2000 3259 3268
23. E.R. Davidson J.J. Gajewski J Am Chem Soc 119 1997 10543 10544
24. H.T. Osterheld J.I. Brauman J Am Chem Soc 115 1993 10311 10316
25. V. Bakken J.M. Millam H.B. Schlegel J Chem Phys 111 1999 8773 8777
26. J.M. Millam V. Bakken W. Chen W.L. Hase H.B. Schlegel J Chem Phys 111 1999 3800 3805
27. S. Anand H.B. Schlegel Phys Chem Chem Phys 6 2004 5166 5171
28. J.A. Nummela B.K. Carpenter J Am Chem Soc 124 2002 8512 8513
29. A.E. Litovitz I. Keresztes B.K. Carpenter J Am Chem Soc 130 2008 12085 12094
30. M.V. Basilevski V.M. Ryaboy Chem Phys Lett 129 1986 71 75
31. H. Tachikawa M. Igarashi Chem Phys Lett 303 1999 81 86
32. L. Sun K. Song W.L. Hase Science 296 2002 875 878
33. W.R. Roth D. Wollweber R. Offerhaus V. Rekowski H.W. Lennartz R. Sustmann Chem Ber 126 1993 2701 2715
34. D.A. Hrovat J.A. Duncan W.T. Borden J Am Chem Soc 121 1999 169 175
35. S.L. Debbert B.K. Carpenter D.A. Hrovat W.T. Borden J Am Chem Soc 124 2002 7896 7897
36. C.D. Berweger W.F. Gunsteren F. Müller-Plathe Angew Chem Int Ed 38 1999 2609 2611
37. C.D. Berweger W.F. Gunsteren F. Müller-Plathe J Chem Phys 108 1998 8773 8781
38. S.J. Blanksby G.B. Ellison B.V. Bierbaum S. Kato J Am Chem Soc 124 2002 3196 3197
39. J.G. López G. Vayner U. Lourderaj S.V. Addepalli S. Kato W.A. de Jong J Am Chem Soc 129 2007 9976 9985
40. D.J. Mann W.L. Hase J Am Chem Soc 124 2002 3208 3209
41. S.C. Ammal H. Yamataka M. Aida M. Dupuis Science 299 2003 1555 1557
42. F.P. Wilgis T.E. Neumann V.J. Shiner Jr. J Am Chem Soc 112 1990 4435 4446
43. T. Bekele C.F. Christian M.A. Lipton D.A. Singleton J Am Chem Soc 127 2005 9216
44. M. Hamaguchi M. Nakaishi T. Nagai T. Nakamura M. Abe J Am Chem Soc 129 2007 12981 12988
45. K.K.-W. Shen R.G. Bergman J Am Chem Soc 99 1977 1655 1657
46. D. Townsend S.A. Lahankar S.K. Lee S.D. Chambreau A.G. Suits X. Zhang Science 306 2004 1158 1161
47. J. Mikosch S. Trippel C. Eichhorn R. Otto U. Lourderaj J.X. Zhang Science 319 2008 183 186
48. A. Pomerantz J.P. Camden A.S. Chioiu F. Ausfelder N. Chawia W.L. Hase J Am Chem Soc 127 2005 16368 16389
49. H. Metiu J. Ross R. Silbey T.F. George J Chem Phys 61 1974 3200 3209
50. J. Baker P.M.W. Gill J Comput Chem 9 1988 465 475
51. E. Bosch M. Moreno J.M. Lluch J. Bertrán Chem Phys Lett 160 1989 543 548
52. W. Quapp M. Hirsch D. Heidrich Theor Chem Acc 100 1998 285 299
53. M. Hirsch W. Quapp D. Heidrich Phys Chem Chem Phys 1 1999 5291 5299
54. M.-N. Ramquet G. Dive D. Dehareng J Chem Phys 112 2000 4923 4934
55. W. Quapp M. Hirsch D. Heidrich Theor Chem Acc 112 2004 40 45 and references cited therein
56. D.A. Singleton C. Hang M.J. Szymanski M.P. Meyer A.G. Leach K.T. Kuwata J Am Chem Soc 125 2003 1319 1328
57. À. Gonzalez-Lafont M. Moreno J.M. Lluch J Am Chem Soc 126 2004 13089 13094
58. D.A. Singleton C. Hang M.J. Syzmanski E.J. Greenwald Am Chem Soc 125 2003 1176 1177
59. A.G. Leach K.N. Houk C.S. Foote J Org Chem 73 2008 8511 8519
60. S.C. Ammal H. Yamataka Eur J Org Chem 2006 4327 4330
61. P. Valtazanos S.T. Elbert K. Ruedenberg J Am Chem Soc 108 1986 3147 3149
62. T. Taketsugu T. Yanai K. Hirao M.S. Gordon J Mol Struct (Theochem) 451 1998 163 177
63. T. Taketsugu M.S. Gordon J Phys Chem 99 1995 8462 8471
64. C. Zhou D.M. Birney Org Lett 4 2002 3279 3282
65. S. Shaik D. Danovich G.N. Sastry P.Y. Ayala H.B. Schlegel J Am Chem Soc 119 1997 9237 9245
66. G.N. Sastry S. Shaik J Am Chem Soc 120 1998 2131 2145
67. G.N. Sastry S. Shaik J Phys Chem 100 1996 12241 12252
68. G.N. Sastry D. Danovich S. Shaik Angew Chem Int Ed 35 1996 1098 1100
69. J. Bertran I. Gallardo G. Morene J.-M. Savéant J Am Chem Soc 118 1996 5737 5744
70. H. Yamataka M. Aida M. Dupuis Chem Phys Lett 300 1999 583 587
71. H. Yamataka M. Aida M. Dupuis Chem Phys Lett 353 2002 310 316
72. H. Yamataka M. Aida M. Dupuis J Phys Org Chem 16 2003 475 483
73. V. Bakken D. Danovich S. Shaik H.B. Schlegel J Am Chem Soc 123 2001 130 134
74. J. Li X. Li S. Shaik H.B. Schlegel J Phys Chem A 108 2004 8526 8532
75. J. Li S. Shaik H.B. Schlegel J Phys Chem A 110 2006 2801 2806
76. T.L. Windus M.S. Gordon L.W. Burggraf L.P. Davis J Am Chem Soc 113 1991 4356 4357
77. T.L. Windus M.S. Gordon Theor Chim Acta 83 1992 21 30
78. T. Yanai T. Taketsugu K. Hirao J Chem Phys 107 1997 1137 1146
79. T. Taketsugu N. Tajima K. Hirao J Chem Phys 105 1996 1933 1939
80. Y. Kumeda T. Taketsugu J Chem Phys 113 2000 477 484
81. O. Castaño R. Palmeiro L.M. Frutos J. Luisandrés J Comput Chem 23 2002 732 736
82. T. Taketsugu T. Hirano J Chem Phys 99 1993 9806 9814
83. T. Taketsugu Y. Kumeda J Chem Phys 114 2001 6973 6982
84. W.A. Krauss A.E. Depristo Theor Chim Acta 69 1986 309 322
85. P. Caramella P. Quadrelli L. Toma J Am Chem Soc 124 2002 1130 1131
86. N. Çelebi-Ölçüm D.H. Ess V. Aviyente K.N. Houk J Org Chem 73 2008 7472 7480
87. B.R. Ussing C. Hang D.A. Singleton J Am Chem Soc 128 2006 7594 7607
88. S.C. Ammal H. Yamataka How does carbocation stability control the beckmann rearrangement reaction? K.K. Laali Recent developments in carbocation and onium ion chemistry, ACS Symposium series Vol. 965 2007 American Chemical Society New York Chapter 17
89. C.P. Suhrada S. Selçuki M. Nendel C. Cannizzaro K.N. Houk P.-J. Rissing Angew Chem Int Ed 44 2005 3548 3552
90. Yamataka H, Sato M, Hasegawa H, Ammal SC. Faraday Discussion 145, in press.
91. S. Yamabe T. Dai T. Minato T. Machiguchi T. Hasegawa J Am Chem Soc 118 1996 6518 6519
92. T. Machiguchi T. Hasegawa A. Ishiwata S. Terashima S. Yamabe T. Minato J Am Chem Soc 121 1999 4771 4786
93. C.A. Grob H.P. Fischer W. Raudenbusch J. Zergenyi Helv Chim Act 47 1964 1003 1021
94. J.E. Leffler Science 117 1953 340 341
95. G.S. Hammond J Am Chem Soc 77 1955 334 338
96. E.R. Thornton J Am Chem Soc 89 1967 2915 2927
97. G.H. Peslherbe H. Wang W.L. Hase J Am Chem Soc 118 1996 2257 2266
98. G.H. Peslherbe H. Wang W.L. Hase J Chem Phys 102 1995 5626 5635 and references cited herein
99. G. Li W.L. Hase J Am Chem Soc 121 1999 7124 7129
100. M. Aida H. Yamataka M. Dupuis Chem Phys Lett 292 1998 474 480
101. M. Aida H. Yamataka M. Dupuis Theor Chem Acc 102 1999 262 271
102. M. Sato H. Yamataka Y. Komeiji Y. Mochizuki T. Ishikawa T. Nakano J Am Chem Soc 130 2008 2396 2397
103. L. Sun W.L. Hase K. Song J Am Chem Soc 123 2001 5753 5756
104. L. Sun E. Chang K. Song W.L. Hase Can J Chem 82 2004 891 899
105. S. Cheon K. Song W.L. Hase THEOCHEM 771 2006 27 31
106. H. Tachikawa J Phys Chem A 104 2000 497 503
107. H. Tachikawa J Phys Chem A 105 2001 1260 1266
108. H. Tachikawa J Chem Phys 125 2006 133119/1–10
109. K. Ingold Structure and mechanism in organic chemistry 2nd ed. 1969 Cornell University Press London
110. H. Yamataka M. Aida Chem Phys Lett 289 1998 105 109
111. T. Nymand K.V. Mikkelsen P.-O. Astrand G.D. Billing Acta Chem Scand 53 1999 1043 1053
112. H.-H. Bueker T. Helgaker K. Ruud E. Uggerud J Phys Chem 100 1996 15388 15392
113. D. Wei D.R. Salahub J Chem Phys 106 1997 6086 6094
114. Y. Ishikawa R.C. Binning Jr. Chem Phys Lett 338 2001 353 360
115. Y. Ishikawa R.C. Binning Jr. Chem Phys Lett 343 2001 597 603
116. A. Furuhama M. Dupuis K. Hirao J Chem Phys 124 2006 164310/1–10
117. Y. Kumeda Y. Minami K. Takano T. Taketsugu T. Hirano J Mol Struct (Theochem) 458 1999 285 291
118. T. Helgaker E. Uggerud H.J.A. Jensen Chem Phys Lett 173 1990 145 150
119. E. Uggerud T. Helgaker J Am Chem Soc 114 1992 4265
120. W. Chen W.L. Hase H.B. Schlegel Chem Phys Lett 228 1994 436 442
121. T. Takayanagi Y. Kurosaki H. Tachikawa Int J Mass Spect 176 1998 227 235
122. K. Bolton W.L. Hase H.B. Schlegel K. Song Chem Phys Lett 288 1998 621 627
123. K. Bolton H.B. Schlegel W.L. Hase K. Song Phys Chem Chem Phys 1 1999 999 1011
124. H. Tachikawa Phys Chem Chem Phys 2 2000 839 845
125. X. Li J.M. Millam H.B. Schlegel J Chem Phys 113 2000 10062 10067
126. K.M. Forsythe S.K. Gray S.J. Klippenstein G.E. Hall J Chem Phys 115 2001 2134 2145
127. L. Sun W.L. Hase J Chem Phys 121 2004 8831 8845
128. B.R. Ussing D.A. Singleton J Am Chem Soc 127 2005 2888 2899
129. Y.J. Cho S.R. Vande Linde L. Zhu W.L. Hase J Chem Phys 96 1992 8275 8287
130. R.L. Hayes E. Fattal N. Govind E.A. Carter J Am Chem Soc 123 2001 641 657
131. A. Tongraar K.R. Lield B.M. Rode Chem Phys Lett 286 1998 56 64
132. M. Garcia-Viloca À. Gona´lez-Lafont J.M. Lluch J Am Chem Soc 121 1999 9198 9207
133. A. Tongraar K. Sagarik B.M. Rode J Phys Chem B 105 2001 10559 10564
134. I. Tuñón M.T.C. Martins-Costa C. Millot M.F. Ruiz-López J Chem Phys 106 1977 3633 3642
135. P. Intharathep A. Tongraar K. Sagarik J Comput Chem 27 2006 1723 1732
136. M. Garcia-Vioca À. Gonza´les-Lafont J.M. Lluch J Am Chem Soc 123 2001 709 721
137. D.P. Geerke S. Thiel W. Thiel W.F. van Gunsteren J Chem Theory Comput 3 2007 1499 1509
138. D.T. Major D.M. York J. Gao J Am Chem Soc 127 2005 16374 16375
139. M. Roca S. Mart J. Andrés V. Moliner I. Tuñón J. Bertrán J Am Chem Soc 125 2003 7726 7737
140. L. Ridder I.M.C. Rietjens J. Vervoort A.J. Mulholland J Am Chem Soc 124 2002 9926 9936
141. H. Hu Z. Lu J.M. Parks S.K. Burger W. Yang J Chem Phys 128 2008 034105-1–034105-18.
142. M. Nagaoka Y. Nagae Y. Koyano Y. Oishi J Phys Chem A 110 2006 4555 4563 and referenced cited therein
143. S.-Y. Yang I. Hristov P. Fleurat-Lessard T. Ziegler J Phys Chem A 109 2005 197 204
144. K. Kitaura E. Ikeo T. Asada T. Nakano M. Uebayasi Chem Phys Lett 313 1999 701 706
145. Y. Komeiji T. Nakanno K. Fukuzawa Y. Ueno Y. Inadomi T. Nemoto Chem Phys Lett 372 2003 342 347
146. Y. Mochizuki Y. Komeiji T. Ishikawa T. Nakano H. Yamataka Chem Phys Lett 437 2007 66 72