-
1
-
-
0038497542
-
-
(reprinted in Ann NY Acad Sci 1995, 758, 737)
-
(a) Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737 (reprinted in Ann NY Acad Sci 1995, 758, 737).
-
(1953)
Nature
, vol.171
, pp. 737
-
-
Watson, J.D.1
Crick, F.H.C.2
-
14
-
-
0003766745
-
-
The C(A)-H ⋯ O(T) hydrogen bond is rather weak: MacMillan: London
-
The C(A)-H ⋯ O(T) hydrogen bond is rather weak: (a) Green, R. D. Hydrogen Bonding by C-H Groups; MacMillan: London, 1974.
-
(1974)
Hydrogen Bonding by C-H Groups
-
-
Green, R.D.1
-
19
-
-
0000080240
-
-
Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P. R., Eds. Wiley: Chichester
-
(d) Del Bene, J. E. In The Encyclopedia of Computational Chemistry, Vol. 2. In: Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P. R., Eds. Wiley: Chichester, 1998; p. 1263.
-
(1998)
In The Encyclopedia of Computational Chemistry
, vol.2
, pp. 1263
-
-
Del Bene, J.E.1
-
21
-
-
0003889315
-
In recent theoretical and experimental advances in hydrogen bonded clusters
-
Xantheas, S. S., Ed.; Kluwer: Dordrecht
-
(f) Del Bene, J. E In Recent Theoretical and Experimental Advances in Hydrogen Bonded Clusters, NATO ASI Series C, Vol. 561, Xantheas, S. S., Ed.; Kluwer: Dordrecht, 2000; p. 309.
-
(2000)
NATO ASI Series C
, vol.561
, pp. 309
-
-
Del Bene, J.E.1
-
24
-
-
0026602512
-
-
(c) Nishio, H.; Ono, A.; Matsuda, A.; Ueda, T. Nucleic Acids Res. 1992, 20, 777.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 777
-
-
Nishio, H.1
Ono, A.2
Matsuda, A.3
Ueda, T.4
-
27
-
-
0023154067
-
-
(c) Sowers, L. C.; Shaw, B. R.; Veigl, M. L.; Sedwick, W. D. Mutation Res 1987, 177, 201.
-
(1987)
Mutation Res
, vol.177
, pp. 201
-
-
Sowers, L.C.1
Shaw, B.R.2
Veigl, M.L.3
Sedwick, W.D.4
-
31
-
-
0000410010
-
-
Clementi, E.; Sarma, R. H., Eds.; Adenine Press: New York
-
(g) Rein, R.; Shibata, M.; Garduno-Juarez, R.; Kieber-Emmons, T. In Structure and Dynamics: Nucleic Acids and Proteins, Clementi, E.; Sarma, R. H., Eds.; Adenine Press: New York, 1983, p. 269.
-
(1983)
Structure and Dynamics: Nucleic Acids and Proteins
, pp. 269
-
-
Rein, R.1
Shibata, M.2
Garduno-Juarez, R.3
Kieber-Emmons, T.4
-
32
-
-
0032546518
-
-
(h) Lutz, M. J.; Horlacher, J.; Benner, S. A. Bioorg Med Chem Lett 1998, 8, 1149.
-
(1998)
Bioorg Med Chem Lett
, vol.8
, pp. 1149
-
-
Lutz, M.J.1
Horlacher, J.2
Benner, S.A.3
-
36
-
-
0003275864
-
-
(a) Kwiatkowski, J. S.; Zielinski, T. J.; Rein, R. Adv Quantum Chem 1986, 18, 85.
-
(1986)
Adv Quantum Chem
, vol.18
, pp. 85
-
-
Kwiatkowski, J.S.1
Zielinski, T.J.2
Rein, R.3
-
37
-
-
0000388278
-
-
Beveridge, D.; Lavery, R., Eds. Adenine Press: New York
-
(b) Kwiatkowski, J. S.; Person, W. B. Theoretical Biochemistry and Molecular Biophysics, Vol. 1: DNA. In: Beveridge, D.; Lavery, R., Eds. Adenine Press: New York, 1990, p. 153.
-
(1990)
Theoretical Biochemistry and Molecular Biophysics, Vol. 1: DNA
, vol.1
, pp. 153
-
-
Kwiatkowski, J.S.1
Person, W.B.2
-
40
-
-
0007436048
-
-
(b) Person, W. B.; Szczepaniak, K.; Szczepaniak, M.; Kwiatkowski, J. S.; Czerminski, R. J. J Mol Struct 1989, 194, 239.
-
(1989)
J Mol Struct
, vol.194
, pp. 239
-
-
Person, W.B.1
Szczepaniak, K.2
Szczepaniak, M.3
Kwiatkowski, J.S.4
Czerminski, R.J.5
-
42
-
-
0029788346
-
-
(d) Šponer, J.; Leszczynski, J.; Hobza, P. J Biomol Struct Dyn 1996, 14, 117.
-
(1996)
J Biomol Struct Dyn
, vol.14
, pp. 117
-
-
Šponer, J.1
Leszczynski, J.2
Hobza, P.3
-
45
-
-
0026318603
-
-
(b) Poltev, V. I.; Teplukhin, A. V.; Kwiatkowski, J. S. J Biomol Struct Dyn 1992, 9, 747.
-
(1992)
J Biomol Struct Dyn
, vol.9
, pp. 747
-
-
Poltev, V.I.1
Teplukhin, A.V.2
Kwiatkowski, J.S.3
-
47
-
-
0000336096
-
-
(b) Morpurgo, S.; Bossa, M.; Morpurgo, G. O. Adv Quantum Chem 2000, 36, 169.
-
(2000)
Adv Quantum Chem
, vol.36
, pp. 169
-
-
Morpurgo, S.1
Bossa, M.2
Morpurgo, G.O.3
-
58
-
-
84987064020
-
-
(i) Kong, Y. S.; Jhon, M. S.; Löwdin, P.-O. Ibid. 1987, 14, 189.
-
(1987)
Int J Quantum Chem Quantum Biol Symp
, vol.14
, pp. 189
-
-
Kong, Y.S.1
Jhon, M.S.2
Löwdin, P.-O.3
-
65
-
-
0000281499
-
-
(b) Clementi, E.; Corongiu, G.; Detrich, J.; Chin, S.; Domingo, L. Int J Quantum Chem: Quantum Chem Symp 1984, 8, 601.
-
(1984)
Int J Quantum Chem: Quantum Chem Symp
, vol.8
, pp. 601
-
-
Clementi, E.1
Corongiu, G.2
Detrich, J.3
Chin, S.4
Domingo, L.5
-
68
-
-
0001536131
-
-
(a) Hrouda, V,; Florián, J.; Hobza, P. J Phys Chem 1993, 97, 1542.
-
(1993)
J Phys Chem
, vol.97
, pp. 1542
-
-
Hrouda, V.1
Florián, J.2
Hobza, P.3
-
69
-
-
0027977295
-
-
(b) Florián, J.; Hrouda, V.; Hobza, P. J Am Chem Soc 1994, 116, 1457.
-
(1994)
J Am Chem Soc
, vol.116
, pp. 1457
-
-
Florián, J.1
Hrouda, V.2
Hobza, P.3
-
72
-
-
33751390857
-
-
(b) Colson, A. O.; Besler, B.; Sevilla, M. D. J Phys Chem 1992, 96, 9787.
-
(1992)
J Phys Chem
, vol.96
, pp. 9787
-
-
Colson, A.O.1
Besler, B.2
Sevilla, M.D.3
-
73
-
-
84962351823
-
-
note
-
All computations were performed at the variety of computational levels using Gaussian 98 suite of packages [18]. The initial optimization was made at HF/6-31+G(d) basis set and was further refined via the single-point calculation employing the Møller-Plesset second-order perturbation theory within the frozen-core approximation (MP2/6-31+G(d)//HF/6-31+G(d)). The third optimization step consisted in using the density functional B3LYP method in conjunction with the same 6-31+G(d) basis set and applied to the minimum energy structures of particular interest. The geometries of the A · T base pair and its proton-transfer structures were fully optimized without any constraint on a possible planarity. The harmonic vibrations were also calculated to locate the minimum energy and transition structures, to analyze their vibrational spectra, and to obtain the thermodynamic quantities, as well. The harmonic frequencies and zero-point vibrational energies (ZPVE) are retained unscaled. The reported energy values are rescaled to the electronic energy E + ZPVE given in kcal/mol unless otherwise noted. Table I and Figure 3 include the energy values corresponding to all employed computational levels.
-
-
-
-
74
-
-
84881454506
-
-
Gaussian: Pittsburgh
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, Jr., J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98 (Revision A.9); Gaussian: Pittsburgh, 1998.
-
(1998)
Gaussian 98 (Revision A.9)
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Zakrzewski, V.G.7
Montgomery J.A., Jr.8
Stratmann, R.E.9
Burant, J.C.10
Dapprich, S.11
Millam, J.M.12
Daniels, A.D.13
Kudin, K.N.14
Strain, M.C.15
Farkas, O.16
Tomasi, J.17
Barone, V.18
Cossi, M.19
Cammi, R.20
Mennucci, B.21
Pomelli, C.22
Adamo, C.23
Clifford, S.24
Ochterski, J.25
Petersson, G.A.26
Ayala, P.Y.27
Cui, Q.28
Morokuma, K.29
Malick, D.K.30
Rabuck, A.D.31
Raghavachari, K.32
Foresman, J.B.33
Cioslowski, J.34
Ortiz, J.V.35
Baboul, A.G.36
Stefanov, B.B.37
Liu, G.38
Liashenko, A.39
Piskorz, P.40
Komaromi, I.41
Gomperts, R.42
Martin, R.L.43
Fox, D.J.44
Keith, T.45
Al-Laham, M.A.46
Peng, C.Y.47
Nanayakkara, A.48
Challacombe, M.49
Gill, P.M.W.50
Johnson, B.51
Chen, W.52
Wong, M.W.53
Andres, J.L.54
Gonzalez, C.55
Head-Gordon, M.56
Replogle, E.S.57
Pople, J.A.58
more..
-
75
-
-
0018471205
-
-
Yanson, I.; Teplitsky, A.; Sukhodub, L. Biopolymers 1979, 18, 1149.
-
(1979)
Biopolymers
, vol.18
, pp. 1149
-
-
Yanson, I.1
Teplitsky, A.2
Sukhodub, L.3
-
78
-
-
84946893847
-
-
(a) Miertus, S.; Scrocco, E.; Tomasi, J. J Chem Phys 1981, 55, 117.
-
(1981)
J Chem Phys
, vol.55
, pp. 117
-
-
Miertus, S.1
Scrocco, E.2
Tomasi, J.3
-
80
-
-
84961981991
-
-
(c) Barone, V.; Cossi, M.; Tomasi, J. Ibid. 1997, 107, 3210.
-
(1997)
J Chem Phys
, vol.107
, pp. 3210
-
-
Barone, V.1
Cossi, M.2
Tomasi, J.3
-
81
-
-
0031553301
-
-
(d) Mennucci, B.; Cances, E.; Tomasi, J. J Phys Chem B 1997, 101, 10506.
-
(1997)
J Phys Chem B
, vol.101
, pp. 10506
-
-
Mennucci, B.1
Cances, E.2
Tomasi, J.3
-
82
-
-
84962338920
-
-
(e) Mennucci, B.; Toniolo, A.; Tomasi, J. J Phys Chem A 2001, 105, 7126.
-
(2001)
J Phys Chem A
, vol.105
, pp. 7126
-
-
Mennucci, B.1
Toniolo, A.2
Tomasi, J.3
-
86
-
-
0023256126
-
-
(d) Gueron, M.; Kochoyan, M.; Leroy, J.-L. Nature 1987, 328, 89.
-
(1987)
Nature
, vol.328
, pp. 89
-
-
Gueron, M.1
Kochoyan, M.2
Leroy, J.-L.3
-
87
-
-
0032739283
-
-
(e) van Aalten, D. M. F.; Erlanson, D. A.; Verdine, G. L.; Josbua-Tor, L. Proc Natl Acad Sci USA 1999, 96, 11809.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11809
-
-
Van Aalten, D.M.F.1
Erlanson, D.A.2
Verdine, G.L.3
Josbua-Tor, L.4
-
88
-
-
0026717833
-
-
(f) Joshua-Tor, L.; Frolow, F.; Appella, E.; Hope, H.; Rabinovich, D.; Sussman, J. L. J Mol Biol 1992, 225, 397.
-
(1992)
J Mol Biol
, vol.225
, pp. 397
-
-
Joshua-Tor, L.1
Frolow, F.2
Appella, E.3
Hope, H.4
Rabinovich, D.5
Sussman, J.L.6
-
89
-
-
0000099235
-
-
(g) Morden, K. M.; Chu, Y. G.; Martin, F. H.; Tinoco, L, Jr. Biochemistry 1983, 22, 5557.
-
(1983)
Biochemistry
, vol.22
, pp. 5557
-
-
Morden, K.M.1
Chu, Y.G.2
Martin, F.H.3
Tinoco L., Jr.4
-
90
-
-
0024965969
-
-
(h) Kalnik, M. W.; Norma, D. G.; Zagorski, M. G.; Swann, P. F.; Patel, D. J. Ibid. 1989, 28, 294.
-
(1989)
Biochemistry
, vol.28
, pp. 294
-
-
Kalnik, M.W.1
Norma, D.G.2
Zagorski, M.G.3
Swann, P.F.4
Patel, D.J.5
-
91
-
-
0013411169
-
-
(a) Keepers, J. W.; Kollman, P. A.; Weiner, P. K.; James, T. L. Proc Natl Acad Sci USA 1982, 79, 5537.
-
(1982)
Proc Natl Acad Sci USA
, vol.79
, pp. 5537
-
-
Keepers, J.W.1
Kollman, P.A.2
Weiner, P.K.3
James, T.L.4
-
93
-
-
0032753202
-
-
(c) Stofer, E.; Chipot, C.; Lavery, R. J Am Chem Soc 1999, 121, 9503.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 9503
-
-
Stofer, E.1
Chipot, C.2
Lavery, R.3
-
95
-
-
0035915260
-
-
(e) Giudice, E.; Várnal, P.; Lavery, R. Chem Phys Chem 2001, 11, 673.
-
(2001)
Chem Phys Chem
, vol.11
, pp. 673
-
-
Giudice, E.1
Várnal, P.2
Lavery, R.3
-
97
-
-
0033573008
-
-
(a) Patikoglou, G. A.; Kim, J. L.; Sun, L.; Yang, S.-H.; Kodadek, T.; Burley, S. K.; Genes Dev 1999, 13, 3217.
-
(1999)
Genes Dev
, vol.13
, pp. 3217
-
-
Patikoglou, G.A.1
Kim, J.L.2
Sun, L.3
Yang, S.-H.4
Kodadek, T.5
Burley, S.K.6
-
98
-
-
0037022570
-
-
and references therein
-
(b) Abrescia, N. G. A.; Thompson, A.; Huynh-Dinh, T.; Subirana, J. A. Proc Natl Acad Sci USA 2002, 99, 2806 and references therein.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 2806
-
-
Abrescia, N.G.A.1
Thompson, A.2
Huynh-Dinh, T.3
Subirana, J.A.4
-
100
-
-
0011824888
-
-
(b) Šponer, J.; Leszczynski, J.; Hobza, P. J Phys Chem 1996, 100, 1965.
-
(1996)
J Phys Chem
, vol.100
, pp. 1965
-
-
Šponer, J.1
Leszczynski, J.2
Hobza, P.3
-
102
-
-
0034639974
-
-
(d) Kratochvil, M.; Šponer, J.; Hobza, P. J Am Chem Soc 2000, 122, 3495.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 3495
-
-
Kratochvil, M.1
Šponer, J.2
Hobza, P.3
-
104
-
-
0035280772
-
-
(b) Kryachko, E. S.; Nguyen, M. T.; Zeegers-Huyskens, Th. Ibid. 2001, 105, 1288, 1934.
-
(2001)
J Phys Chem A
, vol.105
, pp. 1288
-
-
Kryachko, E.S.1
Nguyen, M.T.2
Zeegers-Huyskens, Th.3
-
106
-
-
0033552238
-
-
(b) Gu, Y.; Kar, T.; Scheiner, S. J Am Chem Soc 1999, 121, 9411.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 9411
-
-
Gu, Y.1
Kar, T.2
Scheiner, S.3
-
107
-
-
0034225880
-
-
(c) Hobza, P.; Šponer, J.; Cubero, E.; Orozco, M.; Luque, F. J. J Phys Chem B 2000, 104, 6286.
-
(2000)
J Phys Chem B
, vol.104
, pp. 6286
-
-
Hobza, P.1
Šponer, J.2
Cubero, E.3
Orozco, M.4
Luque, F.J.5
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