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Volumn 39, Issue 2, 2006, Pages 143-150

Computer simulation of proton solvation and transport in aqueous and biomolecular systems

Author keywords

[No Author keywords available]

Indexed keywords

PROTON; PROTON PUMP; SOLVENT; WATER;

EID: 33644989063     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar0402098     Document Type: Article
Times cited : (388)

References (52)
  • 1
  • 2
    • 5944238344 scopus 로고    scopus 로고
    • The quantum dynamics of an excess proton in water
    • Lobaugh, J.; Voth, G. A. The quantum dynamics of an excess proton in water. J. Chem. Phys. 1996, 104, 2056-2069.
    • (1996) J. Chem. Phys. , vol.104 , pp. 2056-2069
    • Lobaugh, J.1    Voth, G.A.2
  • 3
    • 11644271492 scopus 로고    scopus 로고
    • A multi-state empirical valence bond model for proton transport in water
    • Schmitt, U. W.; Voth, G. A. A multi-state empirical valence bond model for proton transport in water. J. Phys. Chem. B 1998, 102, 5547-5551.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 5547-5551
    • Schmitt, U.W.1    Voth, G.A.2
  • 4
    • 0033270702 scopus 로고    scopus 로고
    • Quantum properties of the excess proton in liquid water
    • Schmitt, U. W.; Voth, G. A. Quantum properties of the excess proton in liquid water. Isr. J. Chem. 1999, 39, 483-492.
    • (1999) Isr. J. Chem. , vol.39 , pp. 483-492
    • Schmitt, U.W.1    Voth, G.A.2
  • 5
    • 0001213767 scopus 로고    scopus 로고
    • The computer simulation of proton transport in water
    • Schmitt, U. W.; Voth, G. A. The computer simulation of proton transport in water. J. Chem. Phys. 1999, 111, 9361-9381.
    • (1999) J. Chem. Phys. , vol.111 , pp. 9361-9381
    • Schmitt, U.W.1    Voth, G.A.2
  • 6
    • 0034662848 scopus 로고    scopus 로고
    • A multi-state empirical valence bond model for acid-base chemistry in aqueous solution
    • Cuma, M.; Schmitt, U. W.; Voth, G. A. A multi-state empirical valence bond model for acid-base chemistry in aqueous solution. Chem. Phys. 2000, 258, 187.
    • (2000) Chem. Phys. , vol.258 , pp. 187
    • Cuma, M.1    Schmitt, U.W.2    Voth, G.A.3
  • 7
    • 0002339456 scopus 로고    scopus 로고
    • The isotope substitution effect on the hydrated proton
    • Schmitt, U. W.; Voth, G. A. The isotope substitution effect on the hydrated proton. Chem. Phys. Lett. 2000, 329, 36-41.
    • (2000) Chem. Phys. Lett. , vol.329 , pp. 36-41
    • Schmitt, U.W.1    Voth, G.A.2
  • 8
    • 0034614072 scopus 로고    scopus 로고
    • The mechanism of hydrated proton transport in water
    • Day, T. J. F.; Schmitt, U. W.; Voth, G. A. The mechanism of hydrated proton transport in water. J. Am. Chem. Soc. 2000, 122, 12027-12028.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 12027-12028
    • Day, T.J.F.1    Schmitt, U.W.2    Voth, G.A.3
  • 9
    • 0035967378 scopus 로고    scopus 로고
    • Multi-state empirical valence bond model for weak acid dissociation in aqueous solution
    • Cuma, M.; Schmitt, U. W.; Voth, G. A. Multi-state empirical valence bond model for weak acid dissociation in aqueous solution. J. Phys. Chem. A 2001, 105, 2814-2823.
    • (2001) J. Phys. Chem. A , vol.105 , pp. 2814-2823
    • Cuma, M.1    Schmitt, U.W.2    Voth, G.A.3
  • 10
    • 0037039513 scopus 로고    scopus 로고
    • The vibrational spectrum of the hydrated proton: Comparison of experiment, simulation, and normal-mode analysis
    • Kim, J.; Schmitt, U. W.; Grueetzmacher, J. A.; Voth, G. A.; Scherer, N. F. The vibrational spectrum of the hydrated proton: Comparison of experiment, simulation, and normal-mode analysis. J. Chem. Phys. 2002, 116, 737-746.
    • (2002) J. Chem. Phys. , vol.116 , pp. 737-746
    • Kim, J.1    Schmitt, U.W.2    Grueetzmacher, J.A.3    Voth, G.A.4    Scherer, N.F.5
  • 11
    • 0037159065 scopus 로고    scopus 로고
    • A second generation multistate empirical valence bond model for proton transport in aqueous systems
    • Day, T. J. F.; Soudackov, A. V.; Cuma, M.; Schmitt, U. W.; Voth, G. A. A second generation multistate empirical valence bond model for proton transport in aqueous systems. J. Chem. Phys. 2003, 117, 5839-5849.
    • (2003) J. Chem. Phys. , vol.117 , pp. 5839-5849
    • Day, T.J.F.1    Soudackov, A.V.2    Cuma, M.3    Schmitt, U.W.4    Voth, G.A.5
  • 12
    • 22944484741 scopus 로고    scopus 로고
    • A bond-order analysis of the mechanism for hydrated proton mobility in liquid water
    • No. 014506
    • Lapid, H.; Agmon, N.; Petersen, M. K.; Voth, G. A. A bond-order analysis of the mechanism for hydrated proton mobility in liquid water. J. Chem. Phys. 2004, 122, No. 014506.
    • (2004) J. Chem. Phys. , vol.122
    • Lapid, H.1    Agmon, N.2    Petersen, M.K.3    Voth, G.A.4
  • 13
    • 20844444009 scopus 로고    scopus 로고
    • A linear-scaling self-consistent generalization of the multi-state empirical valence bond model for multiple excess protons in aqueous systems
    • No. 144105
    • Wang, F.; Voth, G. A. A linear-scaling self-consistent generalization of the multi-state empirical valence bond model for multiple excess protons in aqueous systems. J. Chem. Phys. 2005, 122, No. 144105.
    • (2005) J. Chem. Phys. , vol.122
    • Wang, F.1    Voth, G.A.2
  • 14
    • 23844538666 scopus 로고    scopus 로고
    • Ab initio molecular dynamics simulation of aqueous proton solvation and transport revisited
    • No. 044505
    • Izvekov, S.; Voth, G. A. Ab initio molecular dynamics simulation of aqueous proton solvation and transport revisited. J. Chem. Phys. 2005, 123, No. 044505.
    • (2005) J. Chem. Phys. , vol.123
    • Izvekov, S.1    Voth, G.A.2
  • 15
    • 31544469221 scopus 로고    scopus 로고
    • A multi-state empirical valence bond description of protonatable amino acids
    • Maupin, C.; Wong, K. F.; Soudakov, A. V.; Kim, S.; Voth, G. A. A multi-state empirical valence bond description of protonatable amino acids. J. Phys. Chem. B 2006, 110, 631-639.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 631-639
    • Maupin, C.1    Wong, K.F.2    Soudakov, A.V.3    Kim, S.4    Voth, G.A.5
  • 16
    • 6344241179 scopus 로고    scopus 로고
    • The hydrated proton at the water liquid/vapor interface
    • Petersen, M. K.; Iyengar, S. S.; Day, T. J. F.; Voth, G. A. The hydrated proton at the water liquid/vapor interface. J. Phys. Chem. B 2004, 108, 14804-14806.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 14804-14806
    • Petersen, M.K.1    Iyengar, S.S.2    Day, T.J.F.3    Voth, G.A.4
  • 17
    • 15944385626 scopus 로고    scopus 로고
    • On the amphiphilic behavior of the hydrated proton: An ab initio molecular dynamics study
    • Iyengar, S. S.; Day, T. J. F.; Voth, G. A. On the amphiphilic behavior of the hydrated proton: An ab initio molecular dynamics study. Int. J. Mass. Spectrom. 2005, 241, 197-204.
    • (2005) Int. J. Mass. Spectrom. , vol.241 , pp. 197-204
    • Iyengar, S.S.1    Day, T.J.F.2    Voth, G.A.3
  • 19
    • 0035070279 scopus 로고    scopus 로고
    • The formation and dynamics of proton wires in channel environments
    • Brewer, M. L.; Schmitt, U. W.; Voth, G. A. The formation and dynamics of proton wires in channel environments. Biophys. J. 2001, 80, 1691-1702.
    • (2001) Biophys. J. , vol.80 , pp. 1691-1702
    • Brewer, M.L.1    Schmitt, U.W.2    Voth, G.A.3
  • 20
    • 0036197879 scopus 로고    scopus 로고
    • Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane
    • Smondyrev, M.; Voth, G. A. Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. Biophys. J. 2002, 82, 1460-1468.
    • (2002) Biophys. J. , vol.82 , pp. 1460-1468
    • Smondyrev, M.1    Voth, G.A.2
  • 21
    • 17844401731 scopus 로고    scopus 로고
    • Protons may leak through pure lipid bilayers via a concerted mechanism
    • Tepper, H. L.; Voth, G. A. Protons may leak through pure lipid bilayers via a concerted mechanism. Biophys. J. 2005, 88, 3095-3108.
    • (2005) Biophys. J. , vol.88 , pp. 3095-3108
    • Tepper, H.L.1    Voth, G.A.2
  • 22
    • 0036789499 scopus 로고    scopus 로고
    • Molecular dynamics simulation of proton transport through the influenza A virus M2 channel
    • Smondyrev, M.; Voth, G. A. Molecular dynamics simulation of proton transport through the influenza A virus M2 channel. Biophys. J. 2002, 83, 1987-1996.
    • (2002) Biophys. J. , vol.83 , pp. 1987-1996
    • Smondyrev, M.1    Voth, G.A.2
  • 23
    • 0042836529 scopus 로고    scopus 로고
    • Computational studies of proton transport through the M2 channel
    • Wu, Y.; Voth, G. A. Computational studies of proton transport through the M2 channel. FEBS Lett. 2003, 552, 23-27.
    • (2003) FEBS Lett. , vol.552 , pp. 23-27
    • Wu, Y.1    Voth, G.A.2
  • 25
    • 0041843738 scopus 로고    scopus 로고
    • A computer simulation study of the hydrated proton in a synthetic proton channel
    • Wu, Y.; Voth, G. A. A computer simulation study of the hydrated proton in a synthetic proton channel. Biophys. J. 2003, 85, 864-875.
    • (2003) Biophys. J. , vol.85 , pp. 864-875
    • Wu, Y.1    Voth, G.A.2
  • 27
    • 18744381863 scopus 로고    scopus 로고
    • Computer simulation of explicit proton translocation in cytochrome c oxidase: The D-pathway
    • Xu, J.; Voth, G. A. Computer simulation of explicit proton translocation in cytochrome c oxidase: The D-pathway. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6795-6800.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 6795-6800
    • Xu, J.1    Voth, G.A.2
  • 28
    • 3142716193 scopus 로고    scopus 로고
    • The computer simulation of proton transport in biomolecular systems
    • Voth, G. A. The computer simulation of proton transport in biomolecular systems. Front. Biosci. 2003, 8, 1384-1397.
    • (2003) Front. Biosci. , vol.8 , pp. 1384-1397
    • Voth, G.A.1
  • 29
    • 15544364795 scopus 로고    scopus 로고
    • Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane Nafion
    • Petersen, M. K.; Wang, F.; Blake, N. P.; Metiu, H.; Voth, G. A. Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane Nafion. J. Phys. Chem. B 2005, 109, 3727-3730.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 3727-3730
    • Petersen, M.K.1    Wang, F.2    Blake, N.P.3    Metiu, H.4    Voth, G.A.5
  • 31
    • 7644225147 scopus 로고    scopus 로고
    • Molecular dynamics of an excess proton in water using a non-additive valence bond force field
    • Vuilleumier, R.; Borgis, D. Molecular dynamics of an excess proton in water using a non-additive valence bond force field. J. Mol. Struct. 1997, 436, 555-565.
    • (1997) J. Mol. Struct. , vol.436 , pp. 555-565
    • Vuilleumier, R.1    Borgis, D.2
  • 32
    • 0347356002 scopus 로고    scopus 로고
    • Quantum dynamics of an excess proton in water using an extended empirical valence bond Hamiltonian
    • Vuilleumier, R.; Borgis, D. Quantum dynamics of an excess proton in water using an extended empirical valence bond Hamiltonian. J. Phys. Chem. B 1998, 102, 4261.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 4261
    • Vuilleumier, R.1    Borgis, D.2
  • 33
    • 0032548589 scopus 로고    scopus 로고
    • An extended valence bond model for describing proton transfer in H+(H20)n clusters and liquid water
    • Vuilleumier, R.; Borgis, D. An extended valence bond model for describing proton transfer in H+(H20)n clusters and liquid water. Chem. Phys. Lett. 1998, 284, 71.
    • (1998) Chem. Phys. Lett. , vol.284 , pp. 71
    • Vuilleumier, R.1    Borgis, D.2
  • 34
    • 0033264187 scopus 로고    scopus 로고
    • An extended empirical valence bond model for describing proton mobility in water
    • Vuilleumier, R.; Borgis, D. An extended empirical valence bond model for describing proton mobility in water. Isr. J. Chem. 1999, 39, 457.
    • (1999) Isr. J. Chem. , vol.39 , pp. 457
    • Vuilleumier, R.1    Borgis, D.2
  • 35
    • 0347924514 scopus 로고    scopus 로고
    • Transport and spectroscopy of the hydrated proton: A molecular dynamics study
    • Vuilleumier, R.; Borgis, D. Transport and spectroscopy of the hydrated proton: A molecular dynamics study. J. Chem. Phys. 1999, 111, 4251.
    • (1999) J. Chem. Phys. , vol.111 , pp. 4251
    • Vuilleumier, R.1    Borgis, D.2
  • 37
    • 24944460249 scopus 로고    scopus 로고
    • Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water
    • Kim, B.; Young, T.; Harder, E.; Friesner, R. A.; Berne, B. J. Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water. J. Phys. Chem. B 2005, 109, 16529-16538.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 16529-16538
    • Kim, B.1    Young, T.2    Harder, E.3    Friesner, R.A.4    Berne, B.J.5
  • 38
    • 20544467869 scopus 로고    scopus 로고
    • A polarizable empirical valence bond model for proton transport in aqueous solution
    • No. 224507
    • Brancato, G.; Tuckerman, M. E. A polarizable empirical valence bond model for proton transport in aqueous solution. J. Chem. Phys. 2005, 122, No. 224507.
    • (2005) J. Chem. Phys. , vol.122
    • Brancato, G.1    Tuckerman, M.E.2
  • 39
    • 0000135791 scopus 로고
    • Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water
    • Tuckerman, M.; Laasonen, K.; Sprik, M.; Parrinello, M. Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water. J. Chem. Phys. 1995, 103, 150-161.
    • (1995) J. Chem. Phys. , vol.103 , pp. 150-161
    • Tuckerman, M.1    Laasonen, K.2    Sprik, M.3    Parrinello, M.4
  • 40
    • 0031034836 scopus 로고    scopus 로고
    • On the quantum nature of the shared proton in hydrogen bonds
    • Tuckerman, M. E.; Marx, D.; Klein, M. L.; Parrinello, M. On the quantum nature of the shared proton in hydrogen bonds. Science 1997, 275, 817.
    • (1997) Science , vol.275 , pp. 817
    • Tuckerman, M.E.1    Marx, D.2    Klein, M.L.3    Parrinello, M.4
  • 41
    • 0033580290 scopus 로고    scopus 로고
    • The nature of the hydrated excess proton in water
    • Marx, D.; Tuckerman, M. E.; Hutter, J.; Parrinello, M. The nature of the hydrated excess proton in water. Nature 1999, 397, 601.
    • (1999) Nature , vol.397 , pp. 601
    • Marx, D.1    Tuckerman, M.E.2    Hutter, J.3    Parrinello, M.4
  • 42
    • 0346934847 scopus 로고    scopus 로고
    • Free energy of liquid water on the basis of quasichemical theory
    • Asthagiri, D.; Pratt, L R.; Kress, J. D. Free energy of liquid water on the basis of quasichemical theory. Phys. Rev. E 2003, 68, 041505.
    • (2003) Phys. Rev. E , vol.68 , pp. 041505
    • Asthagiri, D.1    Pratt, L.R.2    Kress, J.D.3
  • 43
    • 0942288567 scopus 로고    scopus 로고
    • Towards an assessment of the accuracy of density functional theory for first principles simulations of water
    • Grossman, J. X.; Schwegler, E.; Draeger, E. W.; Gygi, F.; Galli, G. Towards an assessment of the accuracy of density functional theory for first principles simulations of water. J. Chem. Phys. 2004, 120, 300.
    • (2004) J. Chem. Phys. , vol.120 , pp. 300
    • Grossman, J.X.1    Schwegler, E.2    Draeger, E.W.3    Gygi, F.4    Galli, G.5
  • 44
    • 22944439420 scopus 로고    scopus 로고
    • The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water
    • No. 014515
    • VandeVondele, J.; Mohamed, F.; Krack, M.; Hutter, J.; Sprik, M.; Parrinello, M. The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. J. Chem. Phys. 2005, 122, No. 014515.
    • (2005) J. Chem. Phys. , vol.122
    • VandeVondele, J.1    Mohamed, F.2    Krack, M.3    Hutter, J.4    Sprik, M.5    Parrinello, M.6
  • 45
    • 0035504327 scopus 로고    scopus 로고
    • Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)
    • Lill, M. A.; Helms, V. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD). J. Chem. Phys. 2001, 115, 7993-8005.
    • (2001) J. Chem. Phys. , vol.115 , pp. 7993-8005
    • Lill, M.A.1    Helms, V.2
  • 47
    • 0035827187 scopus 로고    scopus 로고
    • Proton transport in polarizable water
    • Walbran, S.; Kornyshev, A. A. Proton transport in polarizable water. J. Chem. Phys. 2001, 114, 10039-10048.
    • (2001) J. Chem. Phys. , vol.114 , pp. 10039-10048
    • Walbran, S.1    Kornyshev, A.A.2
  • 48
    • 0033264221 scopus 로고    scopus 로고
    • Quantum-classical simulation of proton migration in water
    • Zahn, D.; Brickman, J. Quantum-classical simulation of proton migration in water. Isr. J. Chem. 1999, 39, 469-482.
    • (1999) Isr. J. Chem. , vol.39 , pp. 469-482
    • Zahn, D.1    Brickman, J.2
  • 50
    • 11744384413 scopus 로고
    • The Grotthuss mechanism
    • Agmon, N. The Grotthuss mechanism. Chem. Phys. Lett. 1995, 244, 456-462.
    • (1995) Chem. Phys. Lett. , vol.244 , pp. 456-462
    • Agmon, N.1
  • 51
    • 17444439064 scopus 로고    scopus 로고
    • Proton transport through water-filled carbon nanotubes
    • No. 105902
    • Dellago, C.; Naor, M. M.; Hummer, G. Proton transport through water-filled carbon nanotubes. Phys. Rev. Lett. 2003, 90, No. 105902.
    • (2003) Phys. Rev. Lett. , vol.90
    • Dellago, C.1    Naor, M.M.2    Hummer, G.3
  • 52
    • 18444369616 scopus 로고    scopus 로고
    • Evidence for an enhanced hydronium concentration at the liquid water surface
    • Petersen, P. B.; Saykally, R. J. Evidence for an enhanced hydronium concentration at the liquid water surface. J. Phys. Chem. B 2005, 109, 7976-7980.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 7976-7980
    • Petersen, P.B.1    Saykally, R.J.2


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