-
2
-
-
0003534242
-
-
edited by H. H. Mantsch and D. Chapman (Wiley-Liss, New York)
-
Infrared Spectroscopy of Biomolecules, edited by H. H. Mantsch and D. Chapman (Wiley-Liss, New York, 1996).
-
(1996)
Infrared Spectroscopy of Biomolecules
-
-
-
7
-
-
0037021502
-
-
F. Eker, X. Cao, L. Nafie, and R. Schweitzer-Stenner, J. Am. Chem. Soc. 124, 14330 (2002)
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 14330
-
-
Eker, F.1
Cao, X.2
Nafie, L.3
Schweitzer-Stenner, R.4
-
13
-
-
0042594667
-
-
S. Ham, S. Cha, J.-H. Choi, and M. Cho, J. Chem. Phys. 119, 1451 (2003).
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 1451
-
-
Ham, S.1
Cha, S.2
Choi, J.-H.3
Cho, M.4
-
14
-
-
0034684214
-
-
E. S. Manas, Z. Getahun, W. W. Wright, W. F. DeGrado, and J. M. Vanderkooi, J. Am. Chem. Soc. 122, 9883 (2000).
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 9883
-
-
Manas, E.S.1
Getahun, Z.2
Wright, W.W.3
DeGrado, W.F.4
Vanderkooi, J.M.5
-
15
-
-
0031246784
-
-
S. K. Gregurick, E. Fredj, R. Elber, and R. B. Gerber, J. Phys. Chem. B 101, 8595 (1997).
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 8595
-
-
Gregurick, S.K.1
Fredj, E.2
Elber, R.3
Gerber, R.B.4
-
21
-
-
0026656284
-
-
A. Y. Chikishev, G. W. Lucassen, N. I. Koroteev, C. Otto, and J. Greve, Biophys. J. 63, 976 (1992).
-
(1992)
Biophys. J.
, vol.63
, pp. 976
-
-
Chikishev, A.Y.1
Lucassen, G.W.2
Koroteev, N.I.3
Otto, C.4
Greve, J.5
-
23
-
-
0033515091
-
-
P. Hamm, M. Lim, W. F. DeGrado, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. 96, 2036 (1999)
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 2036
-
-
Hamm, P.1
Lim, M.2
DeGrado, W.F.3
Hochstrasser, R.M.4
-
29
-
-
0035949625
-
-
S. Woutersen, Y. Mu, G. Stock, and P. Hamm, Proc. Natl. Acad. Sci. U.S.A. 98, 11254 (2001).
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 11254
-
-
Woutersen, S.1
Mu, Y.2
Stock, G.3
Hamm, P.4
-
30
-
-
0037044485
-
-
S. Woutersen, R. Pfister, P. Hamm, Y. Mu, D. S. Kosov, and G. Stock, J. Chem. Phys. 117, 6833 (2002).
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 6833
-
-
Woutersen, S.1
Pfister, R.2
Hamm, P.3
Mu, Y.4
Kosov, D.S.5
Stock, G.6
-
31
-
-
0041786766
-
-
J. Brendenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, J. Phys. Chem. B 107, 8654 (2003).
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 8654
-
-
Brendenbeck, J.1
Helbing, J.2
Behrendt, R.3
Renner, C.4
Moroder, L.5
Wachtveitl, J.6
Hamm, P.7
-
32
-
-
0035913538
-
-
M. T. Zanni, S. Gnanakaran, Jens Stenger, and R. M. Hochstrasser, J. Phys. Chem. B 105, 6520 (2001).
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6520
-
-
Zanni, M.T.1
Gnanakaran, S.2
Stenger, J.3
Hochstrasser, R.M.4
-
35
-
-
0033647033
-
-
A. Piryatinski, S. Tretiak, V. Chernyak, and S. Mukamel, J. Raman Spectrosc. 31, 125 (2000).
-
(2000)
J. Raman Spectrosc.
, vol.31
, pp. 125
-
-
Piryatinski, A.1
Tretiak, S.2
Chernyak, V.3
Mukamel, S.4
-
37
-
-
0037460526
-
-
A. M. Moran, S.-M. Park, J. Dreyer, and S. Mukamel, J. Chem. Phys. 118, 3651 (2003).
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 3651
-
-
Moran, A.M.1
Park, S.-M.2
Dreyer, J.3
Mukamel, S.4
-
39
-
-
0000742220
-
-
edited by S. H. Lin, A. A. Villaeys, and Y. Fujimura (World Scientific, Singapore)
-
M. Cho, Advances in Multiphon Processes and Spectroscopy, edited by S. H. Lin, A. A. Villaeys, and Y. Fujimura (World Scientific, Singapore, 1999), Vol. 12, p. 229.
-
(1999)
Advances in Multiphon Processes and Spectroscopy
, vol.12
, pp. 229
-
-
Cho, M.1
-
47
-
-
0035873456
-
-
S. Woutersen, Y. Mu, G. Stock, and P. Hamm, Chem. Phys. 266, 137 (2001).
-
(2001)
Chem. Phys.
, vol.266
, pp. 137
-
-
Woutersen, S.1
Mu, Y.2
Stock, G.3
Hamm, P.4
-
48
-
-
37049067243
-
-
G. Eaton, M. C. R. Symons, and P. P. Rastogi, J. Chem. Soc., Faraday Trans. 1 85, 3257 (1989).
-
(1989)
J. Chem. Soc., Faraday Trans. 1
, vol.85
, pp. 3257
-
-
Eaton, G.1
Symons, M.C.R.2
Rastogi, P.P.3
-
49
-
-
0037460569
-
-
S. Ham, J.-H. Kim, H. Lee, and M. Cho, J. Chem. Phys. 118, 3491 (2003).
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 3491
-
-
Ham, S.1
Kim, J.-H.2
Lee, H.3
Cho, M.4
-
52
-
-
0004133516
-
-
Gaussian, Inc., Pittsburgh, Pennsylvania
-
M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 98, Revision A.7, Gaussian, Inc., Pittsburgh, Pennsylvania, 1998.
-
(1998)
GAUSSIAN 98, Revision A.7
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
-
54
-
-
0029011701
-
-
For a detailed discussion on the force field parameters, parm99, the followings papers should be referred to: W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995)
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
56
-
-
3042524904
-
-
C. I. Bayly, P. Cieplak, W. D. Cornell, and P. A. Kollman, J. Phys. Chem. 97, 10269 (1993)
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
57
-
-
0000667030
-
-
W. D. Cornell, P. Cieplak, C. I. Bayly, and P. A. Kollman, J. Am. Chem. Soc. 115, 9620 (1993)
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9620
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollman, P.A.4
-
58
-
-
84986516411
-
-
P. Cieplak, W. D. Cornell, C. Bayly, and P. A. Kollman, J. Comput. Chem. 16, 1357 (1995)
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1357
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.3
Kollman, P.A.4
-
59
-
-
84986532404
-
-
A. St.-Amant, W. D. Cornell, P. A. Kollman, and T. A. Halgren, ibid. 16, 1483 (1995).
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1483
-
-
St.-Amant, A.1
Cornell, W.D.2
Kollman, P.A.3
Halgren, T.A.4
-
61
-
-
33750587438
-
-
H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
62
-
-
1142302456
-
-
note
-
MD simulation method and force field used in the present paper differ from those used by Woutersen et al. in Ref. 39. First of all, the AMBER program with parm99 force field was used in this work, whereas they used the GROMOS program with force field 43Al. However, since the NMA is a relatively rigid molecule unlike other polypeptide molecules, these differences in MD packages and force fields may not induce any notable difference. Secondly, we used no coupling scheme in the production run after the equilibration run at 298 K so that our MD was performed in the NVE condition. On the other hand, they employed the pressure and temperature couplings so that their simulation corresponds to the isothermal-isobaric ensemble. Nevertheless, it is believed that this should not be the reason why their conclusion differs from ours as to the number of H-bonded methanol molecules to the C = O group of the NMA. Thirdly, they used the SHAKE algorithm and their MD time step was 2 fs, whereas we did not use the SHAKE algorithm and our MD time step was 0.5 fs. The latter difference in simulation method is likely to be the reason. Futhermore, the quantum chemistry calculation studies of NMA-methanol clusters, which was presented in Sec. II A, support that the C = O group of the NMA can form two H-bonds with methanol molecules, similar to the cases of NMA-water clusters discussed in Ref. 41.
-
-
-
|