-
3
-
-
0002594455
-
-
(b) Šponer, J.; Leszczynski, J.; Hobza, P. Biopolymers 2002, 61, 3.
-
(2002)
Biopolymers
, vol.61
, pp. 3
-
-
Šponer, J.1
Leszczynski, J.2
Hobza, P.3
-
6
-
-
0001580584
-
-
(c) Les, A.; Adamowicz, L.; Bartlett, R. J. J. Phys. Chem. 1989, 93, 4001.
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 4001
-
-
Les, A.1
Adamowicz, L.2
Bartlett, R.J.3
-
7
-
-
0042117475
-
-
(d) Estrin, D. A.; Paglieri, L.; Corongiu, G. J. Phys. Chem. 1994, 98, 5653.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 5653
-
-
Estrin, D.A.1
Paglieri, L.2
Corongiu, G.3
-
8
-
-
0000462625
-
-
(e) Ha, T. K.; Keller, H. J.; Gunde, R.; Gunthard, H. H. J. Phys. Chem. A 1999, 103, 6612.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 6612
-
-
Ha, T.K.1
Keller, H.J.2
Gunde, R.3
Gunthard, H.H.4
-
9
-
-
0035942929
-
-
(f) Russo, N.; Toscano, M.; Grand, A. J. Phys. Chem. B 2001, 105, 4735.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 4735
-
-
Russo, N.1
Toscano, M.2
Grand, A.3
-
10
-
-
0035944462
-
-
(g) Russo, N.; Toscano, M.; Grand, A. J. Am. Chem. Soc. 2001, 23, 10 272.
-
(2001)
J. Am. Chem. Soc.
, vol.23
, pp. 10272
-
-
Russo, N.1
Toscano, M.2
Grand, A.3
-
11
-
-
30544432269
-
-
(h) Nowak, M. J.; Lapinski, L.; Fulara, J. Spectrochim. Acta Part A 1989, 45, 229.
-
(1989)
Spectrochim. Acta Part A
, vol.45
, pp. 229
-
-
Nowak, M.J.1
Lapinski, L.2
Fulara, J.3
-
13
-
-
0034654078
-
-
van Mourik, T.; Benoit, D. M.; Price, S. L.; Clary, D. C. Phys. Chem. Chem. Phys. 2000, 2, 1281.
-
(2000)
Phys. Chem. Chem. Phys.
, vol.2
, pp. 1281
-
-
Van Mourik, T.1
Benoit, D.M.2
Price, S.L.3
Clary, D.C.4
-
14
-
-
0033927994
-
-
Clary, D. C.; Benoit, D. M.; van Mourik, T. Acc. Chem. Res. 2000, 33, 441.
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 441
-
-
Clary, D.C.1
Benoit, D.M.2
Van Mourik, T.3
-
16
-
-
0001442135
-
-
Sambrano, J. R.; Souza, A. R.; Queralt, J. J.; Andrés, J. Chem. Phys. Lett. 2000, 317, 437.
-
(2000)
Chem. Phys. Lett.
, vol.317
, pp. 437
-
-
Sambrano, J.R.1
Souza, A.R.2
Queralt, J.J.3
Andrés, J.4
-
17
-
-
0035280772
-
-
Kryachko, E. S.; Nguyen, M. T.; Zeegers-Huyskens, T. J. Phys. Chem. A 2001, 105, 1288.
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 1288
-
-
Kryachko, E.S.1
Nguyen, M.T.2
Zeegers-Huyskens, T.3
-
18
-
-
0035869050
-
-
Kryachko, E. S.; Nguyen, M. T.; Zeegers-Huyskens, T. J. Phys. Chem. A 2001, 105, 1934.
-
(2001)
J. Phys. Chem. A.
, vol.105
, pp. 1934
-
-
Kryachko, E.S.1
Nguyen, M.T.2
Zeegers-Huyskens, T.3
-
20
-
-
0037883816
-
-
Carles, S.; Lecomte, F.; Schermann, J. P.; Desfrancois. C. J. Phys. Chem. A 2000, 104, 10 622.
-
(2000)
Desfrancois. C. J. Phys. Chem. A
, vol.104
, pp. 10622
-
-
Carles, S.1
Lecomte, F.2
Schermann, J.P.3
-
22
-
-
84962432615
-
-
Trygubenko, S. A.; Bogdan, T. V.; Rueda, M.; Orozco, M.; Luque, F. J.; Sponer, J.; Slavíčeck, P.; Hobza, P. Phys. Chem. Chem. Phys. 2002, 4, 4192.
-
(2002)
Phys. Chem. Chem. Phys.
, vol.4
, pp. 4192
-
-
Trygubenko, S.A.1
Bogdan, T.V.2
Rueda, M.3
Orozco, M.4
Luque, F.J.5
Sponer, J.6
Slavíčeck, P.7
Hobza, P.8
-
25
-
-
0034645605
-
-
Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V. J. Am. Chem. Soc. 2000, 122, 12 304.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 12304
-
-
Dolgounitcheva, O.1
Zakrzewski, V.G.2
Ortiz, J.V.3
-
27
-
-
0030015253
-
-
Colominas, C.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1996, 118, 6811.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 6811
-
-
Colominas, C.1
Luque, F.J.2
Orozco, M.3
-
28
-
-
4243430048
-
-
Sabio, M.; Topiol, S.; Lumma, W. C. J. Phys. Chem. 1990, 94, 1366
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 1366
-
-
Sabio, M.1
Topiol, S.2
Lumma, W.C.3
-
29
-
-
0001466555
-
-
Szczepaniak, K.; Szczepaniak, M.; Szaida, W.; Person, W. B.; Leszczynski, J. Can. J. Chem. 1991, 69, 1718.
-
(1991)
Can. J. Chem.
, vol.69
, pp. 1718
-
-
Szczepaniak, K.1
Szczepaniak, M.2
Szaida, W.3
Person, W.B.4
Leszczynski, J.5
-
30
-
-
0035879249
-
-
(a) Piuzzi, F.; Mons, M.; Dimicoli, I.; Tardivel, B.; Zhao, Q. Chem. Phys. 2001, 270, 205.
-
(2001)
Chem. Phys.
, vol.270
, pp. 205
-
-
Piuzzi, F.1
Mons, M.2
Dimicoli, I.3
Tardivel, B.4
Zhao, Q.5
-
31
-
-
0037162169
-
-
(b) Mons, M.; Dimicoli, I.; Piuzzi, F.; Tardivel, B.; Elhamine, M. J. Phys. Chem. A 2002, 106, 5088.
-
(2002)
J. Phys. Chem. A
, vol.106
, pp. 5088
-
-
Mons, M.1
Dimicoli, I.2
Piuzzi, F.3
Tardivel, B.4
Elhamine, M.5
-
34
-
-
0004268506
-
-
University of California: San Francisco, CA
-
Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K.; Stanton, R.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R. J.; Siebel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 6; University of California: San Francisco, CA, 1997.
-
(1997)
AMBER 6
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham, T.E.4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.8
Stanton, R.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Ferguson, D.M.13
Radmer, R.J.14
Siebel, G.L.15
Singh, U.C.16
Weiner, P.K.17
Kollman, P.A.18
-
35
-
-
0029633168
-
-
Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Comm. 1995, 91, 43.
-
(1995)
Comput. Phys. Comm.
, vol.91
, pp. 43
-
-
Berendsen, H.J.C.1
Van der Spoel, D.2
Van Drunen, R.3
-
36
-
-
0035789518
-
-
Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Mod. 2001, 7, 306.
-
(2001)
J. Mol. Mod.
, vol.7
, pp. 306
-
-
Lindahl, E.1
Hess, B.2
Van der Spoel, D.3
-
37
-
-
0000008625
-
-
Schleyer, P. v. R., Ed.; John Wiley: Chichester
-
Pearlman, D. A.; Rao, B. G. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Ed.; John Wiley: Chichester, 1998; 1036.
-
(1998)
Encyclopedia of Computational Chemistry
, pp. 1036
-
-
Pearlman, D.A.1
Rao, B.G.2
-
38
-
-
0000249851
-
-
Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529.
-
(1994)
Chem. Phys. Lett.
, vol.222
, pp. 529
-
-
Beutler, T.C.1
Mark, A.E.2
Van Schaik, R.C.3
Gerber, P.R.4
Van Gunsteren, W.F.5
-
39
-
-
20344381993
-
-
Feyereisen, M.; Fitzgerald, G.; Komornicki, A. Chem. Phys. Lett. 1993, 208, 359.
-
(1993)
Chem. Phys. Lett.
, vol.208
, pp. 359
-
-
Feyereisen, M.1
Fitzgerald, G.2
Komornicki, A.3
-
40
-
-
0029011701
-
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. E.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
-
(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, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.E.9
Kollman, P.A.10
-
41
-
-
0034798696
-
-
Jurečka, P.; Nachtigall, P.; Hobza, P. Phys. Chem. Chem. Phys. 2001, 3, 4578.
-
(2001)
Phys. Chem. Chem. Phys.
, vol.3
, pp. 4578
-
-
Jurečka, P.1
Nachtigall, P.2
Hobza, P.3
-
43
-
-
0004133516
-
-
Gaussian, Inc.: Pittsburgh, PA
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, 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.; 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.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998.
-
(1998)
Gaussian 98, Revision A.7
-
-
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.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
Stefanov, B.B.36
Liu, G.37
Liashenko, A.38
Piskorz, P.39
Komaromi, I.40
Gomperts, R.41
Martin, R.L.42
Fox, D.J.43
Keith, T.44
Al-Laham, M.A.45
Peng, C.Y.46
Nanayakkara, A.47
Gonzalez, C.48
Challacombe, M.49
Gill, P.M.W.50
Johnson, B.G.51
Chen, W.52
Wong, M.W.53
Andres, J.L.54
Head-Gordon, M.55
Replogle, E.S.56
Pople, J.A.57
more..
-
45
-
-
4243539377
-
-
Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem. Phys. Lett. 1989, 162, 165.
-
(1989)
Chem. Phys. Lett.
, vol.162
, pp. 165
-
-
Ahlrichs, R.1
Bär, M.2
Häser, M.3
Horn, H.4
Kölmel, C.5
-
47
-
-
3042524904
-
-
Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollmann, P. A. J. Phys. Chem. 1993, 97, 10269.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollmann, P.A.4
-
48
-
-
0037883817
-
-
Mathematica, Wolfram Research, Inc
-
Mathematica, Wolfram Research, Inc.
-
-
-
-
49
-
-
0038221446
-
-
http://www.gromacs.org/contributions/uploaded_contributions/ambconv.tgz.
-
-
-
-
52
-
-
0001430231
-
-
Harvey, S. C.; Tan, R. K. Z.; Cheatham, T. E. J. Comput. Chem. 1998, 19, 726.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 726
-
-
Harvey, S.C.1
Tan, R.K.Z.2
Cheatham, T.E.3
-
55
-
-
0001272783
-
-
Schäfer, H.; Van Gunsteren, W. F.; Mark, E. A. J. Comput. Chem. 1999, 20, 1604.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1604
-
-
Schäfer, H.1
Van Gunsteren, W.F.2
Mark, E.A.3
-
59
-
-
84962428785
-
-
Barone, V.; Cossi, M.; Tomasi, J. J. Comput. Chem. 1998, 19, 404.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 404
-
-
Barone, V.1
Cossi, M.2
Tomasi, J.3
-
60
-
-
0038221440
-
-
note
-
The RI-MP2 dipole moments presented in Table 1 differ only slightly (in tenths of D) from the HF/6-31G* ones used in RESP procedure, and, consequently, also from the dipole moments yielded by the empirical potential. This means that the electrostatic term of the empirical force field (dominant among nonbonded terms) is described adequately.
-
-
-
-
61
-
-
0003653899
-
-
Pearson Education: Harlow
-
Comparing the ab initio relative free energies with the empirical potential ones (cf Table 1) we found a dramatic difference and the latter values are much too large. We were aware of this problem and we presented the gasphase empirical potential relative free energies only to show the convergence of free energy and to estimate the errors bars. Let us further mention that large values of these relative free energies are not an artifact of the code used; the same values were obtained when using the Amber/Gibbs program. The unrealistically large gas-phase free energies are due to two main reasons: first, empirical force field is by definition unable to describe energy changes during a bond creation, annihilation or modification (Leach, A. R. Molecular Modelling, Principles And Applications; Pearson Education: Harlow, 1996; p 194); second, bonded hydrogen atom cannot be described by classical harmonic potential (GROMACS User Manual, version 3.1.1.). The fact that intermolecular free energy changes are often large is known. The solution of the problem mentioned is relatively easy. The values mentioned will cancel when combining different parts of thermodynamic cycle used (Harris, D.; Loew, G. J. Comput. Chem. 1996, 17, 273). Specifically, the intramolecular contribution to the free energy is the same in vacuo and bulk water and is therefore compensated while the remaining contribution (intermolecular one) forms the hydration free energy
-
(1996)
Molecular Modelling, Principles and Applications
, pp. 194
-
-
Leach, A.R.1
-
62
-
-
0000283738
-
-
Comparing the ab initio relative free energies with the empirical potential ones (cf Table 1) we found a dramatic difference and the latter values are much too large. We were aware of this problem and we presented the gasphase empirical potential relative free energies only to show the convergence of free energy and to estimate the errors bars. Let us further mention that large values of these relative free energies are not an artifact of the code used; the same values were obtained when using the Amber/Gibbs program. The unrealistically large gas-phase free energies are due to two main reasons: first, empirical force field is by definition unable to describe energy changes during a bond creation, annihilation or modification (Leach, A. R. Molecular Modelling, Principles And Applications; Pearson Education: Harlow, 1996; p 194); second, bonded hydrogen atom cannot be described by classical harmonic potential (GROMACS User Manual, version 3.1.1.). The fact that intermolecular free energy changes are often large is known. The solution of the problem mentioned is relatively easy. The values mentioned will cancel when combining different parts of thermodynamic cycle used (Harris, D.; Loew, G. J. Comput. Chem. 1996, 17, 273). Specifically, the intramolecular contribution to the free energy is the same in vacuo and bulk water and is therefore compensated while the remaining contribution (intermolecular one) forms the hydration free energy
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 273
-
-
Harris, D.1
Loew, G.2
-
63
-
-
0036974429
-
-
Shishkin, O. V.; Sukhanov, O. S.; Gorb, L.; Leszczynski, J.; Phys. Chem. Chem. Phys. 2002, 4, 5359.
-
(2002)
Phys. Chem. Chem. Phys.
, vol.4
, pp. 5359
-
-
Shishkin, O.V.1
Sukhanov, O.S.2
Gorb, L.3
Leszczynski, J.4
-
65
-
-
0001127721
-
-
McDonald, N. A.; Heather, C. A.; Jorgensen, W. L. J. Phys. Org. Chem. 1997, 10, 563.
-
(1997)
J. Phys. Org. Chem.
, vol.10
, pp. 563
-
-
McDonald, N.A.1
Heather, C.A.2
Jorgensen, W.L.3
-
66
-
-
0038560077
-
-
Schleyer, P. v. R., Ed.: John Wiley: Chichester
-
(a) Pearlman, D. A.; Rao, B. G. In Encyclopedia of Computational Chemistry: Schleyer, P. v. R., Ed.: John Wiley: Chichester, 1998; 1054.
-
(1998)
Encyclopedia of Computational Chemistry
, pp. 1054
-
-
Pearlman, D.A.1
Rao, B.G.2
-
69
-
-
0038560075
-
-
note
-
We are aware of the fact that the direct comparison of the thermodynamic results from Monte Carlo - Free Energy Perturbation approach (used in ref 18) and our present results based on Molecular Dynamics-Thermodynamic Integration is not straightforward. Because the convergence limit was not determined in ref 18 we believe that our data are therefore more reliable. Higher number of sampling windows as well as larger box used in the present study give additional evidence about reliability of our results.
-
-
-
-
70
-
-
0037545996
-
-
note
-
Favorable relative hydration free energy of (7,9) tautomer can be explained on the basis of large stabilization energy with water environment. This is confirmed by large stabilization energies of this tautomer with one and two water molecules. Situation with (3,7) tautomer is different since this form possess only modest dipole moment (contrary to (7,9) having very large dipole moment) and, therefore, its stabilization energy with one and two water molecules is also modest. To explain large hydration free energy we evaluated the temperature dependence of hydration free energy. From the slope of this dependence we calculated the entropy term. At 298.15 K the following estimate was obtained: ΔH(-4 kcal/mol); TΔS(15.5kcal/ mol). Despite the fact that the error in determining the enthalpy and entropy contributions can be significant we must admit that the leading stabilization term is entropic one. For the sake of comparison, we performed the same calculation also for (7,9) tautomer and here the entropy term was found considerably smaller: ΔH(-24 kcal/mol); TΔS(6.5kcal/mol).
-
-
-
-
71
-
-
0037426791
-
-
Jang, Y. H.; Goddard III, W. A.; Noyes, K. T.; Sowers, L. C.; Hwang, S.; Chung, D. S. J. Phys. Chem. B 2003, 107, 344.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 344
-
-
Jang, Y.H.1
Goddard W.A. III2
Noyes, K.T.3
Sowers, L.C.4
Hwang, S.5
Chung, D.S.6
|