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1
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34547774332
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Biological residues containing acylamide units include peptide bonds, asparagine, glutamine, guanine, thymine/uracil, and flavin. The acylamide unit has two tautomers: cis-H and trans-H, as in peptide bonds, asparagine and glutamine, etc., but some only have a cis-H conformer, as in guanine, thymine/uracil, and flavin. In many cases, the cis-H tautomers are located near protein active sites and may play an important role in the functioning of enzymes (refs 2-4).
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Biological residues containing acylamide units include peptide bonds, asparagine, glutamine, guanine, thymine/uracil, and flavin. The acylamide unit has two tautomers: cis-H and trans-H, as in peptide bonds, asparagine and glutamine, etc., but some only have a cis-H conformer, as in guanine, thymine/uracil, and flavin. In many cases, the cis-H tautomers are located near protein active sites and may play an important role in the functioning of enzymes (refs 2-4).
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-
-
3
-
-
0031851483
-
-
(a) Weiss, M. S.; Jabs, A.; Hilgenfeld, R. Nat. Struct. Biol. 1998, 5, 676-676.
-
(1998)
Nat. Struct. Biol
, vol.5
, pp. 676-676
-
-
Weiss, M.S.1
Jabs, A.2
Hilgenfeld, R.3
-
4
-
-
0033548058
-
-
(b) Jabs, A.; Weiss, M. S.; Hilgenfeld, R. J. Mol. Biol. 1999, 286, 291-304.
-
(1999)
J. Mol. Biol
, vol.286
, pp. 291-304
-
-
Jabs, A.1
Weiss, M.S.2
Hilgenfeld, R.3
-
7
-
-
0035857429
-
-
(a) Weatherly, S. C.; Yang, I. V.; Thorp, H. H. J. Am. Chem. Soc. 2001, 123, 1236-1237.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 1236-1237
-
-
Weatherly, S.C.1
Yang, I.V.2
Thorp, H.H.3
-
8
-
-
0035818107
-
-
(b) Shafirovich, V.; Dourandin, A.; Geacintov, N. E. J. Phys. Chem. B 2001, 105, 8431-8435.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 8431-8435
-
-
Shafirovich, V.1
Dourandin, A.2
Geacintov, N.E.3
-
9
-
-
1242276413
-
-
(c) Milligan, J. R.; Aguilera, J. A.; Hoang, O.; Ly, A.; Tran, N. Q.; Ward, J. F. J. Am. Chem. Soc. 2004, 126, 1682-1687.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 1682-1687
-
-
Milligan, J.R.1
Aguilera, J.A.2
Hoang, O.3
Ly, A.4
Tran, N.Q.5
Ward, J.F.6
-
10
-
-
0003880161
-
-
Garland Science: New York
-
Alberts, B.; Bray, D.; Lewis, J.; Raff, M.; Roberts, K.; Watson, J. D. Molecular Biology of the Cell; Garland Science: New York, 2002.
-
(2002)
Molecular Biology of the Cell
-
-
Alberts, B.1
Bray, D.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Watson, J.D.6
-
11
-
-
0032542751
-
-
(a) Cerda, B. A.; Hoyau, S.; Ohanessian, G.; Wesdemiotis, C. J. Am. Chem. Soc. 1998, 120, 2437-2448.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 2437-2448
-
-
Cerda, B.A.1
Hoyau, S.2
Ohanessian, G.3
Wesdemiotis, C.4
-
12
-
-
0034645589
-
-
(b) Kohtani, M.; Kinnear, B. S.; Jarrold, M. F. J. Am. Chem. Soc. 2000, 122, 12377-12378.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 12377-12378
-
-
Kohtani, M.1
Kinnear, B.S.2
Jarrold, M.F.3
-
13
-
-
2242466607
-
-
(c) Wong, C. H. S.; Ma, N. L.; Tsang, C. W. Chem. Eur. J. 2002, 8, 4909-4918.
-
(2002)
Chem. Eur. J
, vol.8
, pp. 4909-4918
-
-
Wong, C.H.S.1
Ma, N.L.2
Tsang, C.W.3
-
16
-
-
33745438253
-
-
(c) Li, H.; Bu, Y.; Yan, S.; Li, P.; Cukier, R. I. J. Phys. Chem. B 2006, 110, 11005-11013.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 11005-11013
-
-
Li, H.1
Bu, Y.2
Yan, S.3
Li, P.4
Cukier, R.I.5
-
17
-
-
0033599290
-
-
(a) Fukuzumi, S.; Patz, M.; Suenobu, T.; Kuwahara, Y.; Itoh, S. J. Am. Chem. Soc. 1999, 121, 1605-1606.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 1605-1606
-
-
Fukuzumi, S.1
Patz, M.2
Suenobu, T.3
Kuwahara, Y.4
Itoh, S.5
-
19
-
-
0035541266
-
-
(c) Ohkubo, K.; Suenobu, T.; Imahori, H.; Orita, A.; Otera. J.; Fukuzumi, S. Chem. Lett. 2001, 30, 978-979.
-
(2001)
Chem. Lett
, vol.30
, pp. 978-979
-
-
Ohkubo, K.1
Suenobu, T.2
Imahori, H.3
Orita, A.4
Otera, J.5
Fukuzumi, S.6
-
20
-
-
0035913970
-
-
(a) Barnett, R. N.; Cleveland, C. L.; Joy, A.; Landman, U.; Schuster, G. B. Science 2001, 294, 567-571.
-
(2001)
Science
, vol.294
, pp. 567-571
-
-
Barnett, R.N.1
Cleveland, C.L.2
Joy, A.3
Landman, U.4
Schuster, G.B.5
-
21
-
-
6944220065
-
-
(b) Ponomarev, S. Y.; Thayer, K. M.; Beveridge, D. L. Proc. Natl. Acad. Sci. U.S. A 2004, 101, 14771-14775.
-
(2004)
Proc. Natl. Acad. Sci. U.S. A
, vol.101
, pp. 14771-14775
-
-
Ponomarev, S.Y.1
Thayer, K.M.2
Beveridge, D.L.3
-
24
-
-
0037747461
-
-
60 may be modulated by changing the metal ions. See also (a) Fukuzumi, S. Org. Biomol. Chem. 2003, 1, 609-620, and references therein.
-
60 may be modulated by changing the metal ions. See also (a) Fukuzumi, S. Org. Biomol. Chem. 2003, 1, 609-620, and references therein.
-
-
-
-
25
-
-
0034804017
-
-
(b) Imahori, H.; Guldi, D. M.; Tamaki, K.; Yoshida, Y.; Luo, C.; Sakata, Y.; Fukuzumi, S. J. Am. Chem. Soc. 2001, 123, 6617-6628.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 6617-6628
-
-
Imahori, H.1
Guldi, D.M.2
Tamaki, K.3
Yoshida, Y.4
Luo, C.5
Sakata, Y.6
Fukuzumi, S.7
-
27
-
-
17744371869
-
-
Isborn, C.; Hrovat, D. A.; Borden, W. T.; Mayer, J. M.; Carpenter, B. K. J. Am. Chem. Soc. 2005, 127, 5794-5795.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 5794-5795
-
-
Isborn, C.1
Hrovat, D.A.2
Borden, W.T.3
Mayer, J.M.4
Carpenter, B.K.5
-
30
-
-
27844469470
-
-
(c) Zhang, J.; Grills, D. C.; Huang, K. W.; Fujita, E.; Bullock, R. M. J. Am. Chem. Soc. 2005, 127, 15684-15685.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 15684-15685
-
-
Zhang, J.1
Grills, D.C.2
Huang, K.W.3
Fujita, E.4
Bullock, R.M.5
-
31
-
-
0035930772
-
-
(a) Roth, J. P.; Yoder, J. C.; Won, T.-J.; Mayer, J. M. Science 2001, 294, 2524-2526.
-
(2001)
Science
, vol.294
, pp. 2524-2526
-
-
Roth, J.P.1
Yoder, J.C.2
Won, T.-J.3
Mayer, J.M.4
-
32
-
-
0344758987
-
-
(b) Tanner, C.; Manca, C.; Leutwyler, S. Science 2003, 302, 1736-1739.
-
(2003)
Science
, vol.302
, pp. 1736-1739
-
-
Tanner, C.1
Manca, C.2
Leutwyler, S.3
-
33
-
-
0037130656
-
-
(a) Mayer, J. M.; Hrovat, D. A.; Thomas, J. L.; Borden, W. T. J. Am. Chem. Soc. 2002, 124, 11142-11147.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 11142-11147
-
-
Mayer, J.M.1
Hrovat, D.A.2
Thomas, J.L.3
Borden, W.T.4
-
34
-
-
3242876557
-
-
(b) Olivella, S.; Anglada, J. M.; Solé, A.; Bofill, J. M. Chem. Eur. J. 2004, 10, 3404-3410.
-
(2004)
Chem. Eur. J
, vol.10
, pp. 3404-3410
-
-
Olivella, S.1
Anglada, J.M.2
Solé, A.3
Bofill, J.M.4
-
40
-
-
33748381480
-
-
(c) Cukier, R. I. J. Phys. Chem. 1996, 100, 15428-15443.
-
(1996)
J. Phys. Chem
, vol.100
, pp. 15428-15443
-
-
Cukier, R.I.1
-
41
-
-
0032561774
-
-
(d) Trammell, S. A.; Wimbish, J. C.; Odobel, F.; Gallagher, L. A.; Narula, P. M.; Meyer, T. J. J. Am. Chem. Soc. 1998, 120, 13248-13249.
-
(1998)
J. Am. Chem. Soc
, vol.120
, pp. 13248-13249
-
-
Trammell, S.A.1
Wimbish, J.C.2
Odobel, F.3
Gallagher, L.A.4
Narula, P.M.5
Meyer, T.J.6
-
46
-
-
0029815959
-
-
(a) Adalsteinsson, H.; Maulitz, A. H.; Bruice, T. C. J. Am. Chem. Soc. 1996, 118, 7689-7693.
-
(1996)
J. Am. Chem. Soc
, vol.118
, pp. 7689-7693
-
-
Adalsteinsson, H.1
Maulitz, A.H.2
Bruice, T.C.3
-
49
-
-
0000356371
-
-
(a) Johansson, A.; Collman, P.; Rothenberg, S.; Mckelvey, J. J. Am. Chem. Soc. 1974, 96, 3794-3800.
-
(1974)
J. Am. Chem. Soc
, vol.96
, pp. 3794-3800
-
-
Johansson, A.1
Collman, P.2
Rothenberg, S.3
Mckelvey, J.4
-
51
-
-
33947093226
-
-
(c) Pullman, A.; Berthod, H.; Giessner-Prettre, C.; Hinton, J. F.; Harpool, D. J. Am. Chem. Soc. 1978, 7, 3991-3994.
-
(1978)
J. Am. Chem. Soc
, vol.7
, pp. 3991-3994
-
-
Pullman, A.1
Berthod, H.2
Giessner-Prettre, C.3
Hinton, J.F.4
Harpool, D.5
-
54
-
-
18344400480
-
-
Muller, A.; Losada, M.; Leutwyler, S. J. Phys. Chem. A 2004, 108, 157-165.
-
(2004)
J. Phys. Chem. A
, vol.108
, pp. 157-165
-
-
Muller, A.1
Losada, M.2
Leutwyler, S.3
-
56
-
-
3142772097
-
-
(b) Ireta, J.; Neugebauer, J.; Scheffler, M. J. Phys. Chem. A 2004, 108, 5692-5698.
-
(2004)
J. Phys. Chem. A
, vol.108
, pp. 5692-5698
-
-
Ireta, J.1
Neugebauer, J.2
Scheffler, M.3
-
59
-
-
0028330140
-
-
(a) Jernigan, R.; Raghunathan, G.; Bahar, I. Curr. Opin. Struct. Biol. 1994, 4, 256-263.
-
(1994)
Curr. Opin. Struct. Biol
, vol.4
, pp. 256-263
-
-
Jernigan, R.1
Raghunathan, G.2
Bahar, I.3
-
64
-
-
34547790991
-
-
Glendening, E. D, Badenhoop, J. K, Reed, A. E, Carpenter, J. E, Bohmann, J. A, Weinhold, F. NBO, version 5.0; Theoretical Chemistry Institute, University of Wisconsin: Madison, WI, 2000
-
(b) Glendening, E. D.; Badenhoop, J. K.; Reed, A. E.; Carpenter, J. E.; Bohmann, J. A.; Weinhold, F. NBO, version 5.0; Theoretical Chemistry Institute, University of Wisconsin: Madison, WI, 2000.
-
-
-
-
65
-
-
0003422992
-
-
2nd ed, Gaussian, Inc, Pittsburgh, PA
-
(c) Foresman, J. B.; Frisch, A. E.; Exploring Chemistry With Electronic Structure Methods, 2nd ed.; Gaussian, Inc.: Pittsburgh, PA, 1996.
-
(1996)
Exploring Chemistry With Electronic Structure Methods
-
-
Foresman, J.B.1
Frisch, A.E.2
-
67
-
-
0011083499
-
-
Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899-926.
-
(1988)
Chem. Rev
, vol.88
, pp. 899-926
-
-
Reed, A.E.1
Curtiss, L.A.2
Weinhold, F.3
-
70
-
-
34547809070
-
-
Gaussian, Inc, Wallingford, CT
-
Frisch, M. J.; et al. Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
-
(2004)
Gaussian 03, Revision
, Issue.C.02
-
-
Frisch, M.J.1
-
72
-
-
0345491105
-
-
(b) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785-789.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
74
-
-
26844534384
-
-
(b) Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. J. Chem. Phys. 1980, 72, 650-654.
-
(1980)
J. Chem. Phys
, vol.72
, pp. 650-654
-
-
Krishnan, R.1
Binkley, J.S.2
Seeger, R.3
Pople, J.A.4
-
75
-
-
84986468715
-
-
(c) Clark, T.; Chandrasekhar, J.; Spitznagel, G. W.; Schleyer, P. v. R. J. Comput. Chem. 1983, 4, 294-301.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 294-301
-
-
Clark, T.1
Chandrasekhar, J.2
Spitznagel, G.W.3
Schleyer, P.V.R.4
-
76
-
-
36549091139
-
-
(d) Frisch, M. J.; Pople, J. A.; Binkley, J. S. J. Chem. Phys. 1984, 80, 3265-3269.
-
(1984)
J. Chem. Phys
, vol.80
, pp. 3265-3269
-
-
Frisch, M.J.1
Pople, J.A.2
Binkley, J.S.3
-
78
-
-
36749113125
-
-
(b) Ishida, K.; Morokuma, K.; Kormornicki, A. J. Chem. Phys. 1977, 66, 2153-2156.
-
(1977)
J. Chem. Phys
, vol.66
, pp. 2153-2156
-
-
Ishida, K.1
Morokuma, K.2
Kormornicki, A.3
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80
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We also estimated the calculational errors for these geometrical parameters and energy quantities by comparing them for FFts at different levels of theory (see Table S4, The deviations among several methods are within 0.05 Å (O⋯O, 0.01 Å (N⋯H⋯N, 0.01 Å (N⋯H, 0.5° (ANHN) for geometrical parameters, and 1.3 kcal/mol (ΔEa, 1.5 kcal/mol (ΔE b, respectively. The deviations of ρN and ρo are almost equal to zero. Together with the calculated geometrical parameters for F Table S3, all these indicate that B3LYP/6-311++G** can yield the reliable results
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o are almost equal to zero. Together with the calculated geometrical parameters for F (Table S3), all these indicate that B3LYP/6-311++G** can yield the reliable results.
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• radical by intramolecular O→N electron transfer, favoring the formation of the cyclic coupling mode with formamide, resulting in a normal HN-H⋯NH two-electron H-bond and a O⋯O three-electron bond.
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• radical by intramolecular O→N electron transfer, favoring the formation of the cyclic coupling mode with formamide, resulting in a normal HN-H⋯NH two-electron H-bond and a O⋯O three-electron bond.
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82
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34547745638
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At the transition state FF,ts, the HOMO is a two-electron π*-antibonding orbital, while the HOMO-2 is a two-electron π-bonding orbital. Both distribute over the whole molecular backbone and may be viewed as linear combinations of two local π orbitals located on two molecular fragments, respectively. The net contribution of their combination to the bonding between two molecular fragments is zero
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ts, the HOMO is a two-electron π*-antibonding orbital, while the HOMO-2 is a two-electron π-bonding orbital. Both distribute over the whole molecular backbone and may be viewed as linear combinations of two local π orbitals located on two molecular fragments, respectively. The net contribution of their combination to the bonding between two molecular fragments is zero.
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We examined the thermodynamics associating with the ligand exchange process: Mz+(H20)n, FF, FF-Mz+(H2O)n-2, 2H2O. The energy changes for three selected hydrated metal ions are exothermic: -18.0 (Ca2, H2O)6, 2.1 (Ca2+(H 2O)7, and -18.5 (Mg2+(H2O) 6) kcal/mol, respectively
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6) kcal/mol, respectively.
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Although the oligohydrates of the metal ions are not predominant species, we can use them to model the hydrated metal ions with large binding energies or Lewis acidity. The binding of these kinds of cations with FF favor HAT. To verify this conclusion, we also examined the effect of a trivalent cation Sc3+ hydrate, FF-Sc3+(H2O)4 (FF+Sc3+(H20)6-FF-Sc3, H2O)4+2H2O) on the FF PT/ET mechanism. Results (at the transition state, ρN3+N10, 0.88, ρo2+o9, 0.12) indicate that FF-Sc3+(H2O)4 obeys the HAT mechanism
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4 obeys the HAT mechanism.
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