메뉴 건너뛰기




Volumn 11, Issue 6, 2015, Pages 2398-2411

Adaptive-Partitioning QM/MM for Molecular Dynamics Simulations: 4. Proton Hopping in Bulk Water

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84931275626     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct501019y     Document Type: Article
Times cited : (50)

References (105)
  • 1
    • 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
  • 2
    • 33748969865 scopus 로고    scopus 로고
    • Proton transfer 200 years after von Grotthuss: Insights from ab initio simulations
    • Marx, D. Proton transfer 200 years after von Grotthuss: Insights from ab initio simulations ChemPhysChem 2006, 7, 1848-1870
    • (2006) ChemPhysChem , vol.7 , pp. 1848-1870
    • Marx, D.1
  • 3
    • 36749115718 scopus 로고
    • Polarization model for water and its ionic dissociation products
    • Stillinger, F. H.; David, C. W. Polarization model for water and its ionic dissociation products J. Chem. Phys. 1978, 69, 1473-1484
    • (1978) J. Chem. Phys. , vol.69 , pp. 1473-1484
    • Stillinger, F.H.1    David, C.W.2
  • 4
    • 0000503651 scopus 로고    scopus 로고
    • A variable charge central force model for water and its ionic dissociation products
    • David, C. W. A variable charge central force model for water and its ionic dissociation products J. Chem. Phys. 1996, 104, 7255-7260
    • (1996) J. Chem. Phys. , vol.104 , pp. 7255-7260
    • David, C.W.1
  • 5
    • 4344583378 scopus 로고
    • A polarizable, dissociating molecular dynamics model for liquid water
    • Halley, J. W.; Rustad, J. R.; Rahman, A. A polarizable, dissociating molecular dynamics model for liquid water J. Chem. Phys. 1993, 98, 4110-4119
    • (1993) J. Chem. Phys. , vol.98 , pp. 4110-4119
    • Halley, J.W.1    Rustad, J.R.2    Rahman, A.3
  • 6
    • 0000817115 scopus 로고    scopus 로고
    • Protonizable water model for quantum dynamical simulations
    • Billeter, S. R.; van Gunsteren, W. F. Protonizable water model for quantum dynamical simulations J. Phys. Chem. A 1998, 102, 4669-4678
    • (1998) J. Phys. Chem. A , vol.102 , pp. 4669-4678
    • Billeter, S.R.1    Van Gunsteren, W.F.2
  • 7
    • 0242678321 scopus 로고    scopus 로고
    • A fully polarizable and dissociable potential for water
    • Lussetti, E.; Pastore, G.; Smargiassi, E. A fully polarizable and dissociable potential for water Chem. Phys. Lett. 2003, 381, 287-291
    • (2003) Chem. Phys. Lett. , vol.381 , pp. 287-291
    • Lussetti, E.1    Pastore, G.2    Smargiassi, E.3
  • 8
    • 34548275482 scopus 로고    scopus 로고
    • Dissociative water potential for molecular dynamics simulations
    • Mahadevan, T. S.; Garofalini, S. H. Dissociative water potential for molecular dynamics simulations J. Phys. Chem. B 2007, 111, 8919-8927
    • (2007) J. Phys. Chem. B , vol.111 , pp. 8919-8927
    • Mahadevan, T.S.1    Garofalini, S.H.2
  • 9
  • 10
    • 77955326111 scopus 로고    scopus 로고
    • A reactive molecular dynamics algorithm for proton transport in aqueous systems
    • Selvan, M. E.; Keffer, D. J.; Cui, S.; Paddison, S. J. A reactive molecular dynamics algorithm for proton transport in aqueous systems J. Phys. Chem. C 2010, 114, 11965-11976
    • (2010) J. Phys. Chem. C , vol.114 , pp. 11965-11976
    • Selvan, M.E.1    Keffer, D.J.2    Cui, S.3    Paddison, S.J.4
  • 11
    • 80755181758 scopus 로고    scopus 로고
    • Lewis-inspired representation of dissociable water in clusters and Grotthuss chains
    • Kale, S.; Herzfeld, J.; Dai, S.; Blank, M. Lewis-inspired representation of dissociable water in clusters and Grotthuss chains J. Biol. Phys. 2012, 38, 49-59
    • (2012) J. Biol. Phys. , vol.38 , pp. 49-59
    • Kale, S.1    Herzfeld, J.2    Dai, S.3    Blank, M.4
  • 12
    • 84894264773 scopus 로고    scopus 로고
    • Explicit proton transfer in classical molecular dynamics simulations
    • Wolf, M. G.; Groenhof, G. Explicit proton transfer in classical molecular dynamics simulations J. Comput. Chem. 2014, 35, 657-671
    • (2014) J. Comput. Chem. , vol.35 , pp. 657-671
    • Wolf, M.G.1    Groenhof, G.2
  • 13
    • 0001060589 scopus 로고    scopus 로고
    • An empirical valence bond model for proton transfer in water
    • Sagnella, D. E.; Tuckerman, M. E. An empirical valence bond model for proton transfer in water J. Chem. Phys. 1998, 108, 2073/1-11
    • (1998) J. Chem. Phys. , vol.108 , pp. 20731-207311
    • Sagnella, D.E.1    Tuckerman, M.E.2
  • 14
    • 11644271492 scopus 로고    scopus 로고
    • Multistate empirical valence bond model for proton transport in water
    • Schmitt, U. W.; Voth, G. A. Multistate 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
  • 15
    • 0032548589 scopus 로고    scopus 로고
    • An extended empirical valence bond model for describing proton transfer in H+(H2O)n clusters and liquid water
    • Vuilleumier, R.; Borgis, D. An extended empirical valence bond model for describing proton transfer in H+(H2O)n clusters and liquid water Chem. Phys. Lett. 1998, 284, 71-77
    • (1998) Chem. Phys. Lett. , vol.284 , pp. 71-77
    • Vuilleumier, R.1    Borgis, D.2
  • 16
    • 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, 4251-4266
    • (1999) J. Chem. Phys. , vol.111 , pp. 4251-4266
    • Vuilleumier, R.1    Borgis, D.2
  • 17
    • 0035913514 scopus 로고    scopus 로고
    • A multistate empirical valence bond approach to a polarizable and flexible water model
    • Lefohn, A. E.; Ovchinnikov, M.; Voth, G. A. A multistate empirical valence bond approach to a polarizable and flexible water model J. Phys. Chem. B 2001, 105, 6628-6637
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6628-6637
    • Lefohn, A.E.1    Ovchinnikov, M.2    Voth, G.A.3
  • 19
    • 20544467869 scopus 로고    scopus 로고
    • A polarizable multistate empirical valence bond model for proton transport in aqueous solution
    • Brancato, G.; Tuckerman, M. E. A polarizable multistate empirical valence bond model for proton transport in aqueous solution J. Chem. Phys. 2005, 122, 224507/1-11
    • (2005) J. Chem. Phys. , vol.122 , pp. 2245071-22450711
    • Brancato, G.1    Tuckerman, M.E.2
  • 20
    • 34249092919 scopus 로고    scopus 로고
    • Proton solvation and transport in aqueous and biomolecular systems: Insights from computer simulations
    • Swanson, J. M. J.; Maupin, C. M.; Chen, H.; Petersen, M. K.; Xu, J.; Wu, Y.; Voth, G. A. Proton solvation and transport in aqueous and biomolecular systems: Insights from computer simulations J. Phys. Chem. B 2007, 111, 4300-4314
    • (2007) J. Phys. Chem. B , vol.111 , pp. 4300-4314
    • Swanson, J.M.J.1    Maupin, C.M.2    Chen, H.3    Petersen, M.K.4    Xu, J.5    Wu, Y.6    Voth, G.A.7
  • 21
    • 49649120885 scopus 로고    scopus 로고
    • Special pair dance and partner selection: Elementary steps in proton transport in liquid water
    • Markovitch, O.; Chen, H.; Izvekov, S.; Paesani, F.; Voth, G. A.; Agmon, N. Special pair dance and partner selection: Elementary steps in proton transport in liquid water J. Phys. Chem. B 2008, 112, 9456-9466
    • (2008) J. Phys. Chem. B , vol.112 , pp. 9456-9466
    • Markovitch, O.1    Chen, H.2    Izvekov, S.3    Paesani, F.4    Voth, G.A.5    Agmon, N.6
  • 22
    • 38749111812 scopus 로고    scopus 로고
    • An improved multistate empirical valence bond model for aqueous proton solvation and transport
    • Wu, Y. J.; Chen, H. N.; Wang, F.; Paesani, F.; Voth, G. A. An improved multistate empirical valence bond model for aqueous proton solvation and transport J. Phys. Chem. B 2008, 112, 467-482
    • (2008) J. Phys. Chem. B , vol.112 , pp. 467-482
    • Wu, Y.J.1    Chen, H.N.2    Wang, F.3    Paesani, F.4    Voth, G.A.5
  • 23
    • 84855861103 scopus 로고    scopus 로고
    • A refined MS-EVB model for proton transport in aqueous environments
    • Park, K.; Lin, W.; Paesani, F. A refined MS-EVB model for proton transport in aqueous environments J. Phys. Chem. B 2012, 116, 343-352
    • (2012) J. Phys. Chem. B , vol.116 , pp. 343-352
    • Park, K.1    Lin, W.2    Paesani, F.3
  • 24
    • 84904569840 scopus 로고    scopus 로고
    • Proton transport under external applied voltage
    • Cao, Z.; Kumar, R.; Peng, Y.; Voth, G. A. Proton transport under external applied voltage J. Phys. Chem. B 2014, 118, 8090-8098
    • (2014) J. Phys. Chem. B , vol.118 , pp. 8090-8098
    • Cao, Z.1    Kumar, R.2    Peng, Y.3    Voth, G.A.4
  • 25
    • 84904562002 scopus 로고    scopus 로고
    • Fast and slow proton transfer in ice: The role of the quasi-liquid layer and hydrogen-bond network
    • Park, K.; Lin, W.; Paesani, F. Fast and slow proton transfer in ice: The role of the quasi-liquid layer and hydrogen-bond network J. Phys. Chem. B 2014, 118, 8081-8089
    • (2014) J. Phys. Chem. B , vol.118 , pp. 8081-8089
    • Park, K.1    Lin, W.2    Paesani, F.3
  • 27
    • 0542436236 scopus 로고
    • Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- Ions in Water
    • Tuckerman, M.; Laasonen, K.; Sprik, M.; Parrinello, M. Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- Ions in Water J. Phys. Chem. 1995, 99, 5749-5752
    • (1995) J. Phys. Chem. , vol.99 , pp. 5749-5752
    • Tuckerman, M.1    Laasonen, K.2    Sprik, M.3    Parrinello, M.4
  • 28
    • 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, 601-604
    • (1999) Nature , vol.397 , pp. 601-604
    • Marx, D.1    Tuckerman, M.E.2    Hutter, J.3    Parrinello, M.4
  • 29
    • 0000181212 scopus 로고    scopus 로고
    • Solvated excess protons in water: quantum effects on the hydration structure
    • Marx, D.; Tuckerman, M. E.; Parrinello, M. Solvated excess protons in water: quantum effects on the hydration structure J. Phys.: Condens. Matter 2000, 12, A153-A159
    • (2000) J. Phys.: Condens. Matter , vol.12 , pp. A153-A159
    • Marx, D.1    Tuckerman, M.E.2    Parrinello, M.3
  • 30
    • 18744399310 scopus 로고    scopus 로고
    • Ab initio molecular dynamics and quasichemical study of H+(aq)
    • Asthagiri, D.; Pratt, L. R.; Kress, J. D. Ab initio molecular dynamics and quasichemical study of H+(aq) Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6704-6708
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 6704-6708
    • Asthagiri, D.1    Pratt, L.R.2    Kress, J.D.3
  • 31
    • 34948872680 scopus 로고    scopus 로고
    • Connecting solvation shell structure to proton transport kinetics in hydrogen-bonded networks via population correlation functions
    • Chandra, A.; Tuckerman, M. E.; Marx, D. Connecting solvation shell structure to proton transport kinetics in hydrogen-bonded networks via population correlation functions Phys. Rev. Lett. 2007, 99, 145901/1-4
    • (2007) Phys. Rev. Lett. , vol.99 , pp. 1459011-1459014
    • Chandra, A.1    Tuckerman, M.E.2    Marx, D.3
  • 32
    • 70849128249 scopus 로고    scopus 로고
    • Concerted hydrogen-bond dynamics in the transport mechanism of the hydrated proton: A first-principles molecular dynamics study
    • Berkelbach, T. C.; Lee, H.-S.; Tuckerman, M. E. Concerted hydrogen-bond dynamics in the transport mechanism of the hydrated proton: A first-principles molecular dynamics study Phys. Rev. Lett. 2009, 103, 238302/1-4
    • (2009) Phys. Rev. Lett. , vol.103 , pp. 2383021-2383024
    • Berkelbach, T.C.1    Lee, H.-S.2    Tuckerman, M.E.3
  • 33
    • 65249172519 scopus 로고    scopus 로고
    • Role of charge transfer in the structure and dynamics of the hydrated proton
    • Swanson, J. M. J.; Simons, J. Role of charge transfer in the structure and dynamics of the hydrated proton J. Phys. Chem. B 2009, 113, 5149-5161
    • (2009) J. Phys. Chem. B , vol.113 , pp. 5149-5161
    • Swanson, J.M.J.1    Simons, J.2
  • 34
    • 77957730975 scopus 로고    scopus 로고
    • A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases
    • Tuckerman, M. E.; Chandra, A.; Marx, D. A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases J. Chem. Phys. 2010, 133, 124108/1-22
    • (2010) J. Chem. Phys. , vol.133 , pp. 1241081-12410822
    • Tuckerman, M.E.1    Chandra, A.2    Marx, D.3
  • 36
    • 84913593376 scopus 로고    scopus 로고
    • The role of quantum effects on structural and electronic fluctuations in neat and charged water
    • Giberti, F.; Hassanali, A. A.; Ceriotti, M.; Parrinello, M. The role of quantum effects on structural and electronic fluctuations in neat and charged water J. Phys. Chem. B 2014, 118, 13226-13235
    • (2014) J. Phys. Chem. B , vol.118 , pp. 13226-13235
    • Giberti, F.1    Hassanali, A.A.2    Ceriotti, M.3    Parrinello, M.4
  • 37
    • 4243606192 scopus 로고
    • Unified approach for molecular dynamics and density-functional theory
    • Car, R.; Parrinello, M. Unified approach for molecular dynamics and density-functional theory Phys. Rev. Lett. 1985, 55, 2471-2474
    • (1985) Phys. Rev. Lett. , vol.55 , pp. 2471-2474
    • Car, R.1    Parrinello, M.2
  • 38
    • 33845595256 scopus 로고    scopus 로고
    • "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis
    • Riccardi, D.; Konig, P.; Prat-Resina, X.; Yu, H. B.; Elstner, M.; Frauenheim, T.; Cui, Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis J. Am. Chem. Soc. 2006, 128, 16302-16311
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 16302-16311
    • Riccardi, D.1    Konig, P.2    Prat-Resina, X.3    Yu, H.B.4    Elstner, M.5    Frauenheim, T.6    Cui, Q.7
  • 40
    • 77952678644 scopus 로고    scopus 로고
    • Application of the SCC-DFTB method to H+(H2O)6, H+(H2O)21, and H+(H2O)22
    • Choi, T. H.; Jordan, K. D. Application of the SCC-DFTB method to H+(H2O)6, H+(H2O)21, and H+(H2O)22 J. Phys. Chem. B 2010, 114, 6932-6936
    • (2010) J. Phys. Chem. B , vol.114 , pp. 6932-6936
    • Choi, T.H.1    Jordan, K.D.2
  • 41
    • 78651286289 scopus 로고    scopus 로고
    • Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields
    • Korth, M. Third-generation hydrogen-bonding corrections for semiempirical QM methods and force fields J. Chem. Theory Comput. 2010, 6, 3808-3816
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 3808-3816
    • Korth, M.1
  • 42
    • 77952687068 scopus 로고    scopus 로고
    • The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: Benchmark simulations
    • Maupin, C. M.; Aradi, B. l.; Voth, G. A. The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: Benchmark simulations J. Phys. Chem. B 2010, 114, 6922-6931
    • (2010) J. Phys. Chem. B , vol.114 , pp. 6922-6931
    • Maupin, C.M.1    Aradi, B.L.2    Voth, G.A.3
  • 43
    • 79958088797 scopus 로고    scopus 로고
    • Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water
    • Goyal, P.; Elstner, M.; Cui, Q. Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water J. Phys. Chem. B 2011, 115, 6790-6805
    • (2011) J. Phys. Chem. B , vol.115 , pp. 6790-6805
    • Goyal, P.1    Elstner, M.2    Cui, Q.3
  • 44
  • 45
    • 84879086750 scopus 로고    scopus 로고
    • Specific reaction path Hamiltonian for proton transfer in water: Reparameterized semiempirical models
    • Wu, X.; Thiel, W.; Pezeshki, S.; Lin, H. Specific reaction path Hamiltonian for proton transfer in water: Reparameterized semiempirical models J. Chem. Theory Comput. 2013, 9, 2672-2686
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 2672-2686
    • Wu, X.1    Thiel, W.2    Pezeshki, S.3    Lin, H.4
  • 46
    • 84907467876 scopus 로고    scopus 로고
    • Molecular simulation of water and hydration effects in different environments: Challenges and developments for DFTB based models
    • Goyal, P.; Qian, H.-J.; Irle, S.; Lu, X.; Roston, D.; Mori, T.; Elstner, M.; Cui, Q. Molecular simulation of water and hydration effects in different environments: Challenges and developments for DFTB based models J. Phys. Chem. B 2014, 118, 11007-11027
    • (2014) J. Phys. Chem. B , vol.118 , pp. 11007-11027
    • Goyal, P.1    Qian, H.-J.2    Irle, S.3    Lu, X.4    Roston, D.5    Mori, T.6    Elstner, M.7    Cui, Q.8
  • 47
    • 84906217744 scopus 로고    scopus 로고
    • Development of semiempirical models for proton transfer reactions in water
    • Wang, S.; MacKay, L.; Lamoureux, G. Development of semiempirical models for proton transfer reactions in water J. Chem. Theory Comput. 2014, 10, 2881-2890
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 2881-2890
    • Wang, S.1    Mackay, L.2    Lamoureux, G.3
  • 48
    • 0017100947 scopus 로고
    • Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
    • Warshel, A.; Levitt, M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme J. Mol. Biol. 1976, 103, 227-249
    • (1976) J. Mol. Biol. , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 49
    • 84988053595 scopus 로고
    • A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl- exchange reaction and gas phase protonation of polyethers
    • Singh, U. C.; Kollmann, P. A. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl- exchange reaction and gas phase protonation of polyethers J. Comput. Chem. 1986, 7, 718-730
    • (1986) J. Comput. Chem. , vol.7 , pp. 718-730
    • Singh, U.C.1    Kollmann, P.A.2
  • 50
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • Field, M. J.; Bash, P. A.; Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J. Comput. Chem. 1990, 11, 700-733
    • (1990) J. Comput. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 51
    • 84962367344 scopus 로고    scopus 로고
    • Methods and applications of combined quantum mechanical and molecular mechanical potentials
    • Gao, J. Methods and applications of combined quantum mechanical and molecular mechanical potentials Rev. Comput. Chem. 1996, 7, 119-185
    • (1996) Rev. Comput. Chem. , vol.7 , pp. 119-185
    • Gao, J.1
  • 52
    • 0032054613 scopus 로고    scopus 로고
    • Quantum mechanical calculations on biological systems
    • Friesner, R. A.; Beachy, M. D. Quantum mechanical calculations on biological systems Curr. Opin. Struct. Biol. 1998, 8, 257-262
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 257-262
    • Friesner, R.A.1    Beachy, M.D.2
  • 54
    • 0001135663 scopus 로고    scopus 로고
    • Combined quantum mechanics and molecular mechanics approaches to chemical and biochemical reactivity
    • von Ragué Schleyer, P. Wiley: Chichester
    • Ruiz-López, M. F.; Rivail, J. L. Combined quantum mechanics and molecular mechanics approaches to chemical and biochemical reactivity In Encyclopedia of computational chemistry, von Ragué Schleyer, P., Ed.; Wiley: Chichester, 1998; Vol. 1, pp 437-448.
    • (1998) Encyclopedia of computational chemistry , vol.1 , pp. 437-448
    • Ruiz-López, M.F.1    Rivail, J.L.2
  • 55
    • 0032711930 scopus 로고    scopus 로고
    • Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
    • Monard, G.; Merz, K. M., Jr. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems Acc. Chem. Res. 1999, 32, 904-911
    • (1999) Acc. Chem. Res. , vol.32 , pp. 904-911
    • Monard, G.1    Merz, K.M.2
  • 56
    • 0033597059 scopus 로고    scopus 로고
    • Chemical reactivity studied by hybrid QM/MM methods
    • Hillier, I. H. Chemical reactivity studied by hybrid QM/MM methods J. Mol. Struct.: THEOCHEM 1999, 463, 45-52
    • (1999) J. Mol. Struct.: THEOCHEM , vol.463 , pp. 45-52
    • Hillier, I.H.1
  • 57
    • 0034859929 scopus 로고    scopus 로고
    • Theoretical perspectives on proton-coupled electron transfer reactions
    • Hammes-Schiffer, S. Theoretical perspectives on proton-coupled electron transfer reactions Acc. Chem. Res. 2000, 34, 273-281
    • (2000) Acc. Chem. Res. , vol.34 , pp. 273-281
    • Hammes-Schiffer, S.1
  • 58
    • 0012576082 scopus 로고    scopus 로고
    • Hybrid quantum mechanics/molecular mechanics approaches
    • Grotendorst, J. John von Neumann-Instituts: Jülich, Germany
    • Sherwood, P. Hybrid quantum mechanics/molecular mechanics approaches. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; John von Neumann-Instituts: Jülich, Germany, 2000; Vol. 3, pp 285-305.
    • (2000) Modern Methods and Algorithms of Quantum Chemistry , vol.3 , pp. 285-305
    • Sherwood, P.1
  • 59
    • 0036025446 scopus 로고    scopus 로고
    • Quantum mechanical methods for enzyme kinetics
    • Gao, J.; Truhlar, D. G. Quantum mechanical methods for enzyme kinetics Annu. Rev. Phys. Chem. 2002, 53, 467-505
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 467-505
    • Gao, J.1    Truhlar, D.G.2
  • 60
    • 0037098212 scopus 로고    scopus 로고
    • New challenges in quantum chemistry: quests for accurate calculations for large molecular systems
    • Morokuma, K. New challenges in quantum chemistry: quests for accurate calculations for large molecular systems Philos. Trans. R. Soc., A 2002, 360, 1149-1164
    • (2002) Philos. Trans. R. Soc., A , vol.360 , pp. 1149-1164
    • Morokuma, K.1
  • 62
    • 33748263629 scopus 로고    scopus 로고
    • Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
    • Zhang, Y. Pseudobond ab initio QM/MM approach and its applications to enzyme reactions Theor. Chem. Acc. 2006, 116, 43-50
    • (2006) Theor. Chem. Acc. , vol.116 , pp. 43-50
    • Zhang, Y.1
  • 63
    • 33846570818 scopus 로고    scopus 로고
    • QM/MM: What have we learned, where are we, and where do we go from here?
    • Lin, H.; Truhlar, D. G. QM/MM: What have we learned, where are we, and where do we go from here? Theor. Chem. Acc. 2007, 117, 185-199
    • (2007) Theor. Chem. Acc. , vol.117 , pp. 185-199
    • Lin, H.1    Truhlar, D.G.2
  • 64
    • 34547507515 scopus 로고    scopus 로고
    • QM/MM methods for biological systems
    • Senn, H. M.; Thiel, W. QM/MM methods for biological systems Top. Curr. Chem. 2007, 268, 173-290
    • (2007) Top. Curr. Chem. , vol.268 , pp. 173-290
    • Senn, H.M.1    Thiel, W.2
  • 65
    • 43949083733 scopus 로고    scopus 로고
    • Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
    • Hu, H.; Yang, W. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods Annu. Rev. Phys. Chem. 2008, 59, 573-601
    • (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 573-601
    • Hu, H.1    Yang, W.2
  • 67
    • 84876719258 scopus 로고    scopus 로고
    • Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology
    • van der Kamp, M. W.; Mulholland, A. J. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology Biochemistry 2013, 52, 2708-2728
    • (2013) Biochemistry , vol.52 , pp. 2708-2728
    • Van Der Kamp, M.W.1    Mulholland, A.J.2
  • 68
    • 84926135997 scopus 로고    scopus 로고
    • Recent developments in QM/MM methods towards open-boundary multi-scale simulations
    • Pezeshki, S.; Lin, H. Recent developments in QM/MM methods towards open-boundary multi-scale simulations Mol. Simul. 2014, 41, 168-189
    • (2014) Mol. Simul. , vol.41 , pp. 168-189
    • Pezeshki, S.1    Lin, H.2
  • 69
    • 0030493185 scopus 로고    scopus 로고
    • A QM/MM simulation method applied to the solution of Li+ in liquid ammonia
    • Kerdcharoen, T.; Liedl, K. R.; Rode, B. M. A QM/MM simulation method applied to the solution of Li+ in liquid ammonia Chem. Phys. 1996, 211, 313-323
    • (1996) Chem. Phys. , vol.211 , pp. 313-323
    • Kerdcharoen, T.1    Liedl, K.R.2    Rode, B.M.3
  • 70
    • 0009662619 scopus 로고    scopus 로고
    • ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase
    • Kerdcharoen, T.; Morokuma, K. ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase Chem. Phys. Lett. 2002, 355, 257-262
    • (2002) Chem. Phys. Lett. , vol.355 , pp. 257-262
    • Kerdcharoen, T.1    Morokuma, K.2
  • 71
    • 0037530063 scopus 로고    scopus 로고
    • Combined quantum mechanics and molecular mechanics simulation of Ca2+/ammonia solution based on the ONIOM-XS method: Octahedral coordination and implication to biology
    • Kerdcharoen, T.; Morokuma, K. Combined quantum mechanics and molecular mechanics simulation of Ca2+/ammonia solution based on the ONIOM-XS method: Octahedral coordination and implication to biology J. Chem. Phys. 2003, 118, 8856-8862
    • (2003) J. Chem. Phys. , vol.118 , pp. 8856-8862
    • Kerdcharoen, T.1    Morokuma, K.2
  • 72
    • 33947392043 scopus 로고    scopus 로고
    • Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations
    • Heyden, A.; Lin, H.; Truhlar, D. G. Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations J. Phys. Chem. B 2007, 111, 2231-2241
    • (2007) J. Phys. Chem. B , vol.111 , pp. 2231-2241
    • Heyden, A.1    Lin, H.2    Truhlar, D.G.3
  • 74
    • 77950118237 scopus 로고    scopus 로고
    • Properties of a method for performing adaptive, multilevel QM simulations of complex chemical reactions in the gas-phase
    • Guthrie, M. G.; Daigle, A. D.; Salazar, M. R. Properties of a method for performing adaptive, multilevel QM simulations of complex chemical reactions in the gas-phase J. Chem. Theory Comput. 2010, 6, 18-25
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 18-25
    • Guthrie, M.G.1    Daigle, A.D.2    Salazar, M.R.3
  • 75
    • 77957897253 scopus 로고    scopus 로고
    • Recent progress in adaptive multiscale molecular dynamics simulations of soft matter
    • Nielsen, S. O.; Bulo, R. E.; Moore, P. B.; Ensing, B. Recent progress in adaptive multiscale molecular dynamics simulations of soft matter Phys. Chem. Chem. Phys. 2010, 12, 12401-12414
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 12401-12414
    • Nielsen, S.O.1    Bulo, R.E.2    Moore, P.B.3    Ensing, B.4
  • 76
    • 77953944856 scopus 로고    scopus 로고
    • Classical to path-integral adaptive resolution in molecular simulation: Towards a smooth quantum-classical coupling
    • Poma, A. B.; Delle Site, L. Classical to path-integral adaptive resolution in molecular simulation: Towards a smooth quantum-classical coupling Phys. Rev. Lett. 2010, 104, 250201/1-4
    • (2010) Phys. Rev. Lett. , vol.104 , pp. 2502011-2502014
    • Poma, A.B.1    Delle Site, L.2
  • 77
    • 80755185247 scopus 로고    scopus 로고
    • Adaptive-partitioning redistributed charge and dipole schemes for QM/MM dynamics simulations: On-the-fly relocation of boundaries that pass through covalent bonds
    • Pezeshki, S.; Lin, H. Adaptive-partitioning redistributed charge and dipole schemes for QM/MM dynamics simulations: On-the-fly relocation of boundaries that pass through covalent bonds J. Chem. Theory Comput. 2011, 7, 3625-3634
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3625-3634
    • Pezeshki, S.1    Lin, H.2
  • 79
    • 84865065466 scopus 로고    scopus 로고
    • Application of adaptive QM/MM methods to molecular dynamics simulations of aqueous systems
    • Park, K.; Gotz, A. W.; Walker, R. C.; Paesani, F. Application of adaptive QM/MM methods to molecular dynamics simulations of aqueous systems J. Chem. Theory Comput. 2012, 8, 2868-2877
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2868-2877
    • Park, K.1    Gotz, A.W.2    Walker, R.C.3    Paesani, F.4
  • 80
    • 84856099238 scopus 로고    scopus 로고
    • The number-adaptive multiscale QM/MM molecular dynamics simulation: Application to liquid water
    • Takenaka, N.; Kitamura, Y.; Koyano, Y.; Nagaoka, M. The number-adaptive multiscale QM/MM molecular dynamics simulation: Application to liquid water Chem. Phys. Lett. 2012, 524, 56-61
    • (2012) Chem. Phys. Lett. , vol.524 , pp. 56-61
    • Takenaka, N.1    Kitamura, Y.2    Koyano, Y.3    Nagaoka, M.4
  • 82
    • 84885600912 scopus 로고    scopus 로고
    • Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution
    • Várnai, C.; Bernstein, N.; Mones, L.; Csányi, G. Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution J. Phys. Chem. B 2013, 117, 12202-12211
    • (2013) J. Phys. Chem. B , vol.117 , pp. 12202-12211
    • Várnai, C.1    Bernstein, N.2    Mones, L.3    Csányi, G.4
  • 83
    • 84907980869 scopus 로고    scopus 로고
    • Size-consistent multipartitioning QM/MM: A stable and efficient adaptive QM/MM method
    • Watanabe, H. C.; Kubař, T.; Elstner, M. Size-consistent multipartitioning QM/MM: A stable and efficient adaptive QM/MM method J. Chem. Theory Comput. 2014, 10, 4242-4252
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 4242-4252
    • Watanabe, H.C.1    Kubař, T.2    Elstner, M.3
  • 84
    • 84909638703 scopus 로고    scopus 로고
    • Adaptive-partitioning QM/MM dynamics simulations: 3. Solvent molecules entering and leaving protein binding sites
    • Pezeshki, S.; Davis, C.; Heyden, A.; Lin, H. Adaptive-partitioning QM/MM dynamics simulations: 3. Solvent molecules entering and leaving protein binding sites J. Chem. Theory Comput. 2014, 10, 4765-4776
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 4765-4776
    • Pezeshki, S.1    Davis, C.2    Heyden, A.3    Lin, H.4
  • 85
    • 84908054123 scopus 로고    scopus 로고
    • A density-based adaptive quantum mechanical/molecular mechanical method
    • Waller, M. P.; Kumbhar, S.; Yang, J. A density-based adaptive quantum mechanical/molecular mechanical method ChemPhysChem 2014, 15, 3218-3225
    • (2014) ChemPhysChem , vol.15 , pp. 3218-3225
    • Waller, M.P.1    Kumbhar, S.2    Yang, J.3
  • 87
    • 84867394893 scopus 로고    scopus 로고
    • Combining a dissociative water model with a hybrid QM/MM approach-a simulation strategy for the study of proton transfer reactions in solution
    • Hofer, T. S.; Hitzenberger, M.; Randolf, B. R. Combining a dissociative water model with a hybrid QM/MM approach-a simulation strategy for the study of proton transfer reactions in solution J. Chem. Theory Comput. 2012, 8, 3586-3595
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 3586-3595
    • Hofer, T.S.1    Hitzenberger, M.2    Randolf, B.R.3
  • 90
    • 84931267747 scopus 로고    scopus 로고
    • version 2.0.0.CO; University of Minnesota: Minneapolis, MN
    • Lin, H.; Zhang, Y.; Pezeshki, S.; Truhlar, D. G. QMMM, version 2.0.0.CO; University of Minnesota: Minneapolis, MN, 2015.
    • (2015) QMMM
    • Lin, H.1    Zhang, Y.2    Pezeshki, S.3    Truhlar, D.G.4
  • 91
    • 34247531772 scopus 로고    scopus 로고
    • version 5.1; Washington University: St. Louis, MO
    • Ponder, J. W. TINKER, version 5.1; Washington University: St. Louis, MO, 2010.
    • (2010) TINKER
    • Ponder, J.W.1
  • 92
    • 84874829967 scopus 로고    scopus 로고
    • version 7.0; Max-Planck-Institut für Kohlenforschung: Müheim an der Ruhr, Germany
    • Thiel, W. MNDO2005, version 7.0; Max-Planck-Institut für Kohlenforschung: Müheim an der Ruhr, Germany, 2005.
    • (2005) MNDO2005
    • Thiel, W.1
  • 93
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
    • Stewart, J. P. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements J. Mol. Model. 2007, 13, 1173-1213
    • (2007) J. Mol. Model. , vol.13 , pp. 1173-1213
    • Stewart, J.P.1
  • 94
    • 30744437399 scopus 로고    scopus 로고
    • Flexible simple point-charge water model with improved liquid-state properties
    • Wu, Y.; Tepper, H. L.; Voth, G. A. Flexible simple point-charge water model with improved liquid-state properties J. Chem. Phys. 2006, 124, 024503/1-12
    • (2006) J. Chem. Phys. , vol.124 , pp. 0245031-02450312
    • Wu, Y.1    Tepper, H.L.2    Voth, G.A.3
  • 95
    • 1542779956 scopus 로고    scopus 로고
    • Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
    • Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties Phys. Rev. B 1998, 58, 7260-7268
    • (1998) Phys. Rev. B , vol.58 , pp. 7260-7268
    • Elstner, M.1    Porezag, D.2    Jungnickel, G.3    Elsner, J.4    Haugk, M.5    Frauenheim, T.6    Suhai, S.7    Seifert, G.8
  • 96
    • 0345713551 scopus 로고    scopus 로고
    • Hybrid models for combined quantum mechanical and molecular mechanical approaches
    • Bakowies, D.; Thiel, W. Hybrid models for combined quantum mechanical and molecular mechanical approaches J. Phys. Chem. 1996, 100, 10580-10594
    • (1996) J. Phys. Chem. , vol.100 , pp. 10580-10594
    • Bakowies, D.1    Thiel, W.2
  • 97
    • 18844410543 scopus 로고    scopus 로고
    • Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations
    • Lin, H.; Truhlar, D. G. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations J. Phys. Chem. A 2005, 109, 3991-4004
    • (2005) J. Phys. Chem. A , vol.109 , pp. 3991-4004
    • Lin, H.1    Truhlar, D.G.2
  • 98
    • 36049000840 scopus 로고    scopus 로고
    • Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum-mechanical and molecular-mechanical calculations
    • Zhang, Y.; Lin, H.; Truhlar, D. G. Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum-mechanical and molecular-mechanical calculations J. Chem. Theory Comput. 2007, 3, 1378-1398
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 1378-1398
    • Zhang, Y.1    Lin, H.2    Truhlar, D.G.3
  • 99
    • 58149145247 scopus 로고    scopus 로고
    • Flexible-boundary quantum-mechanical/molecular-mechanical calculations: Partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems
    • Zhang, Y.; Lin, H. Flexible-boundary quantum-mechanical/molecular-mechanical calculations: Partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems J. Chem. Theory Comput. 2008, 4, 414-425
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 414-425
    • Zhang, Y.1    Lin, H.2
  • 100
    • 77954865932 scopus 로고    scopus 로고
    • Flexible-boundary QM/MM calculations: II. Partial charge transfer across the QM/MM boundary that passes through a covalent bond
    • Zhang, Y.; Lin, H. Flexible-boundary QM/MM calculations: II. Partial charge transfer across the QM/MM boundary that passes through a covalent bond Theor. Chem. Acc. 2010, 126, 315-322
    • (2010) Theor. Chem. Acc. , vol.126 , pp. 315-322
    • Zhang, Y.1    Lin, H.2
  • 101
    • 84905588006 scopus 로고    scopus 로고
    • Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems
    • Pezeshki, S.; Lin, H. Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems J. Comput. Chem. 2014, 35, 1778-1788
    • (2014) J. Comput. Chem. , vol.35 , pp. 1778-1788
    • Pezeshki, S.1    Lin, H.2
  • 102
    • 75749094385 scopus 로고    scopus 로고
    • Polarization and charge transfer in the hydration of chloride ions
    • Zhao, Z.; Rogers, D. M.; Beck, T. L. Polarization and charge transfer in the hydration of chloride ions J. Chem. Phys. 2010, 132, 014502/1-10
    • (2010) J. Chem. Phys. , vol.132 , pp. 0145021-01450210
    • Zhao, Z.1    Rogers, D.M.2    Beck, T.L.3
  • 103
    • 85024806135 scopus 로고    scopus 로고
    • The effects of charge transfer on the aqueous solvation of ions
    • Soniat, M.; Rick, S. W. The effects of charge transfer on the aqueous solvation of ions J. Chem. Phys. 2012, 137, 044511/1-9
    • (2012) J. Chem. Phys. , vol.137 , pp. 0445111-0445119
    • Soniat, M.1    Rick, S.W.2
  • 104
    • 84937821520 scopus 로고    scopus 로고
    • Bringing reactivity to the aggregation-volume-bias Monte Carlo based simulation framework: Water nucleation induced by a reactive proton
    • Kumar, R.; Knight, C.; Wick, C. D.; Chen, B. Bringing reactivity to the aggregation-volume-bias Monte Carlo based simulation framework: Water nucleation induced by a reactive proton J. Phys. Chem. B 2014, 10.1021/jp508749x
    • (2014) J. Phys. Chem. B
    • Kumar, R.1    Knight, C.2    Wick, C.D.3    Chen, B.4
  • 105
    • 84904792423 scopus 로고    scopus 로고
    • Charge transfer effects of ions at the liquid water/vapor interface
    • Soniat, M.; Rick, S. W. Charge transfer effects of ions at the liquid water/vapor interface J. Chem. Phys. 2014, 140, 184703/1-10
    • (2014) J. Chem. Phys. , vol.140 , pp. 1847031-18470310
    • Soniat, M.1    Rick, S.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.