Ab initio molecular dynamics study of glycine intramolecular proton transfer in water

Journal of Chemical Physics

Volumn 122, Issue 18, 2005, Pages

  Leung, Kevin ^a   Rempe, Susan B ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CHARGE TRANSFER; CHARGED PARTICLES; CONFORMATIONS; FREE ENERGY; HYDRATION; PROTONS; THERMODYNAMIC PROPERTIES; WATER;

FREE-ENERGY BARRIERS; GLYCINE; HYDRATION NUMBER; PROTON TRANSFER;

MOLECULAR DYNAMICS;

GLYCINE; ION; PROTON; WATER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRICITY; METHODOLOGY; PHYSICAL CHEMISTRY; QUANTUM THEORY; THEORETICAL MODEL; THERMODYNAMICS; TIME;

CHEMISTRY; CHEMISTRY, PHYSICAL; ELECTROSTATICS; GLYCINE; IONS; MODELS, MOLECULAR; MODELS, THEORETICAL; PROTONS; QUANTUM THEORY; THERMODYNAMICS; TIME FACTORS; WATER;

EID: 18844407104     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1885445     Document Type: Article

References (88)

1. K.-D. Kreuer, S. J. Paddison, E. Spohr, and M. Schuster, Chem. Rev. (Washington, D.C.) 104, 4637 (2004).
2. T. E. Decoursey, Physiol. Rev. 83, 475 (2003).
3. I. Andersson and T. C. Taylor, Arch. Biochem. Biophys. 414, 130 (2003).
4. C. M. Nimigean, J. S. Chappie, and C. Miller, Biochemistry 42, 9263 (2003).
5. L. G. Cuello, J. G. Romero, D. M. Cortes, and E. Perozo, Biochemistry 37, 3229 (1998).
6. M. Sprik, J. Phys.: Condens. Matter 12, A161 (2000).
7. I-F. W. Kuo, C. J. Mundy, M. J. McGrath, J. Phys. Chem. B 108, 12990 (2004).
8. I. Ivanov and M. L. Klein, J. Am. Chem. Soc. 124, 13380 (2002).
9. M. Sprik, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/12/8A/318 12, A161 (2000); J. E. Davis, N. L. Doltsinis, A. J. Kirby, C. D. Roussev, and M. Sprik, J. Am. Chem. Soc. 124, 6594 (2002).
10. M. Sprik, J. Phys.: Condens. Matter 0953-8984 10.1088/0953-8984/12/8A/318 12, A161 (2000); J. E. Davis, N. L. Doltsinis, A. J. Kirby, C. D. Roussev, and M. Sprik, J. Am. Chem. Soc. 124, 6594 (2002).
11. P. L. Geissler, C. Dellago, D. Chandler, J. Hutter, and M. Parrinello, Science 291, 2121 (2001).
12. J. Schlitter and M. Klahn, J. Chem. Phys. 118, 2057 (2003).
13. L. R. Pratt and R. A. LaViolette, Mol. Phys. 94, 909 (1998).
14. Theoretically, it has been shown that at least three water molecules are needed to stablize ZW over NF in the gas phase. J. H. Jensen and M. S. Gordon, J. Am. Chem. Soc. 117, 8159 (1995).
15. H. M. Senn, P. M. Margl, R. Schmid, T. Ziegler, and P. E. Blochl, J. Chem. Phys. 118, 1089 (2003); dynamics of the glycine molecule are explicitly treated here.
16. P. Bandyopadhyay, M. S. Gordon, B. Mennucci, and J. Tomasi, J. Chem. Phys. 116, 5023 (2002). A glycine- (H2 O)8 cluster without dielectric continuum correction is also considered in this work.
17. M. Sheinblatt and H. S. Cutowsky, J. Am. Chem. Soc. 86, 4814 (1964).
18. G. Wada, E. Tamura, M. Okina, and M. Nakamura, Bull. Chem. Soc. Jpn. 55, 3064 (1982).
19. K. C. Chang and E. Grunwald, J. Phys. Chem. 80, 1422 (1976).
20. E. Grunwald, K. C. Chang, P. L. Skipper, and V. K. Anderson, J. Phys. Chem. 80, 1425 (1976).
21. M. A. Slifkin and S. M. Ali, J. Mol. Liq. 28, 215 (1984).
22. P. Haberfield, J. Chem. Educ. 57, 346 (1980).
23. Y. Kameda, H. Ebata, T. Usuki, O. Uemura, and M. Misawa, Bull. Chem. Soc. Jpn. 67, 3159 (1994).
24. The designations follow those of A. Császár, J. Am. Chem. Soc. 114, 9568 (1992).
25. Y. Ding and K. Krogh-Jespersen, Chem. Phys. Lett. 199, 261 (1992).
26. S. Xu, J. M. Nilles, and K. H. Bowen, Jr., J. Chem. Phys. 119, 10696 (2003).
27. See A. G. Császár and A. Perczel, Prog. Biophys. Mol. Biol. 71, 243 (1999) for a review of amino acid conformers.
28. S. Sirois, E. I. Proynov, D. T. Nguyen, and D. R. Salahub, J. Chem. Phys. 107, 6770 (1997), and references therein.
29. N. Okuyama-Yoshida, M. Nagaoka, and T. Yamabe, J. Phys. Chem. A 102, 285 (1998).
30. M. Nagaoka, N. Okuyama-Yoshida, and T. Yamabe, J. Phys. Chem. A 102, 8202 (1998).
31. I. Tuñón, E. Silla, and M. F. Ruiz-López, Chem. Phys. Lett. 321, 433 (2000).
32. E. Kassab, J. Langlet, E. Evleth, and Y. Akacem, THEOCHEM 531, 267 (2000).
33. M. E. Tuckerman, D. Marx, and M. Parrinello, Nature (London) 417, 925 (2002).
34. W. L. Jorgensen and J.-L. Gao, J. Phys. Chem. 90, 2174 (1986).
35. F. M. L. G. Stamato and J. M. Goodfellow, Int. J. Quantum Chem., Quantum Biol. Symp. 13, 277 (1986), and references therein.
36. G. Alagona, C. Ghio, and P. A. Kollman, THEOCHEM 166, 385 (1988).
37. G. Alagona, C. Ghio, and P. A. Kollman, J. Am. Chem. Soc. 108, 185 (1986).
38. Computer simulations of aqueous amino acid zwitterions and related species include U. C. Singh, F. K. Brown, P. A. Bash, and P. A. Kollman, J. Am. Chem. Soc. 0002-7863 109, 1607 (1987); P. E. Smith, L. X. Dang, and B. M. Pettitt, J. Am. Chem. Soc. 0002-7863 113, 67 (1991); P. I. Nagy and K. Takács-Novák, J. Am. Chem. Soc. 0002-7863 119, 4999 (1997); D. J. Price, J. D. Roberts, and W. L. Jorgensen, J. Am. Chem. Soc. 0002-7863 10.1021/ja9812397 120, 9672 (1998); and G. E. Marlow and B. M. Pettitt, J. Am. Chem. Soc. 68, 192 (2003).
39. Computer simulations of aqueous amino acid zwitterions and related species include U. C. Singh, F. K. Brown, P. A. Bash, and P. A. Kollman, J. Am. Chem. Soc. 0002-7863 109, 1607 (1987); P. E. Smith, L. X. Dang, and B. M. Pettitt, J. Am. Chem. Soc. 0002-7863 113, 67 (1991); P. I. Nagy and K. Takács-Novák, J. Am. Chem. Soc. 0002-7863 119, 4999 (1997); D. J. Price, J. D. Roberts, and W. L. Jorgensen, J. Am. Chem. Soc. 0002-7863 10.1021/ja9812397 120, 9672 (1998); and G. E. Marlow and B. M. Pettitt, J. Am. Chem. Soc. 68, 192 (2003).
40. Computer simulations of aqueous amino acid zwitterions and related species include U. C. Singh, F. K. Brown, P. A. Bash, and P. A. Kollman, J. Am. Chem. Soc. 0002-7863 109, 1607 (1987); P. E. Smith, L. X. Dang, and B. M. Pettitt, J. Am. Chem. Soc. 0002-7863 113, 67 (1991); P. I. Nagy and K. Takács-Novák, J. Am. Chem. Soc. 0002-7863 119, 4999 (1997); D. J. Price, J. D. Roberts, and W. L. Jorgensen, J. Am. Chem. Soc. 0002-7863 10.1021/ja9812397 120, 9672 (1998); and G. E. Marlow and B. M. Pettitt, J. Am. Chem. Soc. 68, 192 (2003).
41. Computer simulations of aqueous amino acid zwitterions and related species include U. C. Singh, F. K. Brown, P. A. Bash, and P. A. Kollman, J. Am. Chem. Soc. 0002-7863 109, 1607 (1987); P. E. Smith, L. X. Dang, and B. M. Pettitt, J. Am. Chem. Soc. 0002-7863 113, 67 (1991); P. I. Nagy and K. Takács-Novák, J. Am. Chem. Soc. 0002-7863 119, 4999 (1997); D. J. Price, J. D. Roberts, and W. L. Jorgensen, J. Am. Chem. Soc. 0002-7863 10.1021/ja9812397 120, 9672 (1998); and G. E. Marlow and B. M. Pettitt, J. Am. Chem. Soc. 68, 192 (2003).
42. Computer simulations of aqueous amino acid zwitterions and related species include U. C. Singh, F. K. Brown, P. A. Bash, and P. A. Kollman, J. Am. Chem. Soc. 0002-7863 109, 1607 (1987); P. E. Smith, L. X. Dang, and B. M. Pettitt, J. Am. Chem. Soc. 0002-7863 113, 67 (1991); P. I. Nagy and K. Takács-Novák, J. Am. Chem. Soc. 0002-7863 119, 4999 (1997); D. J. Price, J. D. Roberts, and W. L. Jorgensen, J. Am. Chem. Soc. 0002-7863 10.1021/ja9812397 120, 9672 (1998); and G. E. Marlow and B. M. Pettitt, J. Am. Chem. Soc. 68, 192 (2003).
43. J. Gao, J. Am. Chem. Soc. 117, 8600 (1995).
44. Y. Kameda, T. Mori, T. Nishiyama, T. Usuki, and O. Uemura, Bull. Chem. Soc. Jpn. 69, 1495 (1996).
45. Y. Kameda, K. Fukuhara, K. Mochiduki, H. Naganuma, T. Usuki, and O. Uemura, J. Non-Cryst. Solids 312-314, 433 (2002).
46. E. Cubero, F. J. Luque, M. Orozco, and J.-L. Gao, J. Phys. Chem. B 107, 1664 (2003).
47. A. Warshel and M. Levitt, J. Mol. Biol. 0022-2836 10.1016/0022-2836(76) 90311-9 103, 227 (1976); M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990).
48. A. Warshel and M. Levitt, J. Mol. Biol. 0022-2836 10.1016/0022-2836(76) 90311-9 103, 227 (1976); M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990).
49. K. Leung and S. B. Rempe, J. Am. Chem. Soc. 126, 344 (2004).
50. T. Shoeib, G. D. Ruggiero, K. W. M. Siu, A. C. Hopkinson, and I. H. William, J. Chem. Phys. 117, 2762 (2002).
51. A. Fernández-Ramos, Z. Smedarchina, W. Siebrand, and M. Z. Zgierski, J. Chem. Phys. 113, 9714 (2000).
52. L. R. Pratt and S. B. Rempe, in Simulation and Theory of Electrostatic Interactions in Solution, AIP Conf. Proc. No. 492, edited by, L. R. Pratt, and, G. Hummer, (AIP, New York, 1999), pp. 172-201.
53. S. B. Rempe and L. R. Pratt, Fluid Phase Equilib. 183-184, 121 (2001).
54. S. B. Rempe, L. R. Pratt, G. Hummer, J. D. Kress, R. L. Martin, and A. Redondo, J. Am. Chem. Soc. 122, 966 (2000).
55. D. Asthagiri, L. R. Pratt, M. E. Paulaitis, and S. B. Rempe, J. Am. Chem. Soc. 126, 1285 (2004).
56. S. B. Rempe, D. Asthagiri, and L. R. Pratt, Phys. Chem. Chem. Phys. 6, 1966 (2004).
57. J. Hütter, P. Ballone, M. Bernasconi, CPMD Version 3.4, MPI für Festkörperforschung and IBM Research Laboratory, 1990 -1998.
58. A. D. Becke, Phys. Rev. A 38, 3098 (1988).
59. C. T. Lee, W. T. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988).
60. N. Troullier and J. L. Martins, Phys. Rev. B 43, 1993 (1991).
61. F. Bruǵ, M. Bernasconi, and M. Parrinello, J. Am. Chem. Soc. 121, 10883 (1999), and references therein.
62. T. H. Lilley, in The Chemistry and Biochemistry of Amino Acids, edited by, G. C. Barret, (Chapman and Hall, London, 1985).
63. Our fixed volume predictions actually correspond to the Helmholtz free energy. Nevertheless, we will us "ΔG" throughout, because that appears to be the common usage in this field.
64. D. Chandler, Introduction to Modern Statistical Mechanics (Oxford University Press, New York, 1987).
65. As discussed in the text, rotation about the N-C bond renders the three ammonium group protons equivalent. We only observe this rotation, however, when glycine is in the zwitterion form-when the reaction coordinate R<-2 Å. For the other sampling windows, such a rotation cannot occur until R<-2 Å, i.e., unless the system leaves the pertinent sampling windows, which it is prevented from doing by the umbrella sampling constraints on the glycine geometry (Table). So as long as we use an unconstrained ZW window and constrained sampling windows elsewhere, ΔG (R) is unambiguous. This is one reason we elect to use umbrella sampling rather than the more common integration of the constrained force method. For general ways to deal with the deprotonation of atoms with multiple protons attached, M. Sprik, Chem. Phys. 259, 139 (2000).
66. P. Bolhuis and D. Chandler, J. Chem. Phys. 113, 8154 (2000).
67. See the discussions in E. Kassab (Ref. 31) and Ref. 55 therein.
68. K. Toukan and A. Rahman, Phys. Rev. B 31, 2643 (1985).
69. Our plane-wave based QM/MM capability is built into the plane-wave electronic structure code VASP [G. Kresse and J. Furthmüller, Phys. Rev. B 0163-1829 10.1103/PhysRevB.54.11169 54, 11169 (1996); G. Kresse and J. Furthmüller, Comput. Mater. Sci. 0927-0256 10.1016/0927-0256(96)00008-0 6, 15 (1996)]. The QM/MM algorithm is similar to that of A. Laio, J. VandeVondele, and U. Rothlisberger, J. Chem. Phys. 116, 6941 (2002), except that, given the small box size, the QM and MM regions are coupled together directly in Fourier space.
70. Our plane-wave based QM/MM capability is built into the plane-wave electronic structure code VASP [G. Kresse and J. Furthmüller, Phys. Rev. B 0163-1829 10.1103/PhysRevB.54.11169 54, 11169 (1996); G. Kresse and J. Furthmüller, Comput. Mater. Sci. 0927-0256 10.1016/0927-0256(96)00008-0 6, 15 (1996)]. The QM/MM algorithm is similar to that of A. Laio, J. VandeVondele, and U. Rothlisberger, J. Chem. Phys. 116, 6941 (2002), except that, given the small box size, the QM and MM regions are coupled together directly in Fourier space.
71. Our plane-wave based QM/MM capability is built into the plane-wave electronic structure code VASP [G. Kresse and J. Furthmüller, Phys. Rev. B 0163-1829 10.1103/PhysRevB.54.11169 54, 11169 (1996); G. Kresse and J. Furthmüller, Comput. Mater. Sci. 0927-0256 10.1016/0927-0256(96)00008-0 6, 15 (1996)]. The QM/MM algorithm is similar to that of A. Laio, J. VandeVondele, and U. Rothlisberger, J. Chem. Phys. 116, 6941 (2002), except that, given the small box size, the QM and MM regions are coupled together directly in Fourier space.
72. w, is obtained by integrating the pair correlation g(r) of the pertinent atom with the water O or H atom to its first minimum.
73. - groups, which is not observed in our simulations.
74. A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
75. M. J. Frisch, G. W. Trucks, H. B. Schlegel, GAUSSIAN 98, Revision A.2, Gaussian Inc., Pittsburgh, PA, 1998.
76. L. R. Pratt, G. J. Tawa, G. Hummer, A. E. Garcia, and S. A. Corcelli, Int. J. Quantum Chem. 64, 121 (1997); with the radii defined as in E. V. Stefanovich and T. N. Truong, Chem. Phys. Lett. 244, 65 (1995).
77. L. R. Pratt, G. J. Tawa, G. Hummer, A. E. Garcia, and S. A. Corcelli, Int. J. Quantum Chem. 64, 121 (1997); with the radii defined as in E. V. Stefanovich and T. N. Truong, Chem. Phys. Lett. 244, 65 (1995).
78. V. Barone, L. Orlandini, and C. Adamo, Chem. Phys. Lett. 231, 295 (1994).
79. V. Barone, L. Orlandini, and C. Adamo, Int. J. Quantum Chem. 56, 697 (1995).
80. V. Barone and C. Adamo, J. Chem. Phys. 105, 11007 (1996).
81. S. Sadhukhan, D. Muñoz, C. Adamo, and G. E. Scuseria, Chem. Phys. Lett. 83, 306 (1999).
82. D. Sicinska, P. Paneth, and D. G. Truhlar, J. Phys. Chem. B 106, 2708 (2002).
83. - groups, which is not observed in our simulations.
84. L. R. Pratt and S. W. Haan, J. Chem. Phys. 0021-9606 10.1063/1.441276 74, 1864 (1981); L. R. Pratt and S. W. Haan, J. Chem. Phys. 74, 1873 (1981).
85. L. R. Pratt and S. W. Haan, J. Chem. Phys. 0021-9606 10.1063/1.441276 74, 1864 (1981); L. R. Pratt and S. W. Haan, J. Chem. Phys. 74, 1873 (1981).
86. G. Makov and M. C. Payne, Phys. Rev. B 51, 4014 (1995).
87. D. E. Smith and A. D. J. Haymet, Fluid Phase Equilib. 88, 79 (1993).
88. G. Hummer, L. R. Pratt, and A. E. Garcia, J. Phys. Chem. 99, 14188 (1995).