메뉴 건너뛰기




Volumn 1, Issue 1, 2010, Pages 219-223

Compatibility of quantum chemical methods and empirical (MM) water models in quantum mechanics/ molecular mechanics liquid water simulations

Author keywords

General theory; Molecular structure; Quantum chemistry

Indexed keywords

AQUEOUS ENVIRONMENT; BASIS SETS; FREE ENERGY SIMULATIONS; GENERAL THEORY; LIQUID WATER; MONTE CARLO; QM/MM METHOD; QM/MM MODELING; QUANTUM-CHEMICAL METHODS; WATER MODELS; WATER MOLECULE;

EID: 77149168226     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz900096p     Document Type: Article
Times cited : (48)

References (30)
  • 1
    • 0036836445 scopus 로고    scopus 로고
    • A Reappraisal of What We Have Learnt during Three Decades of Computer Simulations on Water
    • Guillot, B. A Reappraisal of What We Have Learnt during Three Decades of Computer Simulations on Water. J. Mol. Liq. 2002,101,219-260.
    • (2002) J. Mol. Liq , vol.101 , pp. 219-260
    • Guillot, B.1
  • 2
    • 18744387415 scopus 로고    scopus 로고
    • Potential Energy Functions for Atomic-Level Simulations of Water and Organic and Biomolecular Systems
    • Jorgensen, W. L.; Tirado-Rives, J. Potential Energy Functions for Atomic-Level Simulations of Water and Organic and Biomolecular Systems. Proc. Natl. Acad. Sci. U.S.A. 2005, 102,6665-6670.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 6665-6670
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 4
    • 33645858780 scopus 로고
    • Quantum and Statistical Mechanical Studies of Liquids 0.10. Transferable Intermolecular Potential Functions for Water, Alcohols, and Ethers - Application to Liquid Water
    • Jorgensen, W.L. Quantum and Statistical Mechanical Studies of Liquids 0.10. Transferable Intermolecular Potential Functions for Water, Alcohols, and Ethers - Application to Liquid Water. J. Am. Chem. Soc. 1981, 103, 335-340.
    • (1981) J. Am. Chem. Soc , vol.103 , pp. 335
    • Jorgensen, W.L.1
  • 6
    • 0000020246 scopus 로고    scopus 로고
    • A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions
    • Mahoney, M. W.; Jorgensen, W. L. A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions. J. Chem. Phys. 2000,112,8910-8922.
    • (2000) J. Chem. Phys , vol.112 , pp. 8910-8922
    • Mahoney, M.W.1    Jorgensen, W.L.2
  • 7
    • 33644968201 scopus 로고    scopus 로고
    • Structural Correlations and Motifs in Liquid Water at Selected Temperatures: Ab Initio and Empirical Model Predictions
    • Mantz, Y. A.; Chen, B.; Martyna, G. J. Structural Correlations and Motifs in Liquid Water at Selected Temperatures: Ab Initio and Empirical Model Predictions. J. Phys. Chem. B 2006, 110,3540-3554.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3540-3554
    • Mantz, Y.A.1    Chen, B.2    Martyna, G.J.3
  • 8
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of Activation Free Energies in Molecular Systems
    • Neria, E.; Fischer, S.; Karplus, M. Simulation of Activation Free Energies in Molecular Systems. J. Chem. Phys. 1996, 105, 1902-1921.
    • (1996) J. Chem. Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 11
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM Methods for Biomolecular Systems
    • Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems. Angew. Chem., Int. Ed. 2009, 48, 1198-1229.
    • (2009) Angew. Chem., Int. Ed , vol.48 , pp. 1198
    • Senn, H.M.1    Thiel, W.2
  • 13
    • 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
  • 15
    • 38049039241 scopus 로고    scopus 로고
    • An Efficient Method forthe Calculation of Quantum Mechanics/Molecular Mechanics Free Energies
    • Woods, C. J.; Manby, F. R.; Mulholland, A. J. An Efficient Method forthe Calculation of Quantum Mechanics/Molecular Mechanics Free Energies. J. Chem. Phys. 2008, 128, 014109-014101.
    • (2008) J. Chem. Phys , vol.128 , pp. 014109-014101
    • Woods, C.J.1    Manby, F.R.2    Mulholland, A.J.3
  • 16
    • 0034317110 scopus 로고    scopus 로고
    • A High-Quality X-ray Scattering Experiment on Liquid Water at Ambient Conditions
    • Hura, G.; Sorenson, J. M.; Glaeser, R. M.; Head-Gordon, T. A High-Quality X-ray Scattering Experiment on Liquid Water at Ambient Conditions. J. Chem. Phys. 2000, 113, 9140-9148.
    • (2000) J. Chem. Phys , vol.113 , pp. 9140-9148
    • Hura, G.1    Sorenson, J.M.2    Glaeser, R.M.3    Head-Gordon, T.4
  • 17
    • 46149133757 scopus 로고
    • A New Determination of the Structure of Water at 25 C
    • Soper, A. K.; Phillips, M. G. A New Determination of the Structure of Water at 25 C. Chem. Phys. 1986, 107, 47-60.
    • (1986) Chem. Phys , vol.107 , pp. 47-60
    • Soper, A.K.1    Phillips, M.G.2
  • 18
    • 2442545593 scopus 로고    scopus 로고
    • Site-Site Pair Correlation Functions of Water from 25 to 400 C: Revised Analysis of New and Old Diffraction Data
    • Soper, A. K.; Bruni, F.; Ricci, M. A. Site-Site Pair Correlation Functions of Water from 25 to 400 C: Revised Analysis of New and Old Diffraction Data. J. Chem. Phys. 1997, 106, 247-254.
    • (1997) J. Chem. Phys , vol.106 , pp. 247-254
    • Soper, A.K.1    Bruni, F.2    Ricci, M.A.3
  • 19
    • 0343017595 scopus 로고
    • Liquid Water-Molecular Correlation Functions from X-ray Diffraction
    • Narten, A. H.; Levy, H. A. Liquid Water-Molecular Correlation Functions from X-ray Diffraction. J.Chem.Phys.1971,55, 2263.
    • (1971) J.chem.phys , vol.55 , pp. 2263
    • Narten, A.H.1    Levy, H.A.2
  • 21
    • 0029864799 scopus 로고    scopus 로고
    • Progress toward Chemical Accuracyin the Computer Simulation of Condensed Phase Reactions
    • Bash, P. A.; Ho, L. L.; MacKerell, A. D.; Levine, D.; Hallstrom, P. Progress toward Chemical Accuracyin the Computer Simulation of Condensed Phase Reactions. Proc. Natl. Acad. Sci. U.S.A. 1996,93,3698-3703.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 3698-3703
    • Bash, P.A.1    Ho, L.L.2    Mackerell, A.D.3    Levine, D.4    Hallstrom, P.5
  • 22
    • 0001041299 scopus 로고    scopus 로고
    • Optimization of the Lennard-Jones Parameters for a Combined Ab Initio Quantum Mechanical and Molecular Mechanical Potential Using the 3-21G Basis Set
    • Freindorf, M.; Gao, J. L. Optimization of the Lennard-Jones Parameters for a Combined Ab Initio Quantum Mechanical and Molecular Mechanical Potential Using the 3-21G Basis Set. J. Comput. Chem. 1996, 17, 386-395.
    • (1996) J. Comput. Chem , vol.17 , pp. 386-395
    • Freindorf, M.1    Gao, J.L.2
  • 23
    • 23844517091 scopus 로고    scopus 로고
    • Lennard-Jones Parameters for the Combined QM/MM Method Using the B3LYP/6-31+G*/AMBER Potential
    • Freindorf, M.; Shao, Y. H.; Furlani, T. R.; Kong, J. Lennard-Jones Parameters for the Combined QM/MM Method Using the B3LYP/6-31+G*/AMBER Potential. J. Comput. Chem. 2005,26,1270-1278.
    • (2005) J. Comput. Chem , vol.26 , pp. 1270-1278
    • Freindorf, M.1    Shao, Y.H.2    Furlani, T.R.3    Kong, J.4
  • 24
    • 0027125907 scopus 로고
    • A Priori Evaluation of Aqueous Polarization Effects through Monte-Carlo QM-MM Simulations
    • Gao, J. L.; Xia, X. F. A Priori Evaluation of Aqueous Polarization Effects through Monte-Carlo QM-MM Simulations. Science 1992, 258, 631-635.
    • (1992) Science , vol.258 , pp. 631-635
    • Gao, J.L.1    Xia, X.F.2
  • 25
    • 0034319693 scopus 로고    scopus 로고
    • Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods
    • Luque, F. J.; Reuter, N.; Cartier, A.; Ruiz-Lopez, M. F. Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods. J. Phys. Chem. A 2000, 104, 10923-10931.
    • (2000) J. Phys. Chem. A , vol.104 , pp. 10923-10931
    • Luque, F.J.1    Reuter, N.2    Cartier, A.3    Ruiz-Lopez, M.F.4
  • 27
    • 2642585833 scopus 로고    scopus 로고
    • Importance of van der Waals Interactions in QM/MM Simulations
    • Riccardi, D.; Li, G. H.; Cui, Q. Importance of van der Waals Interactions in QM/MM Simulations. J. Phys. Chem. B 2004, 108,6467-6478.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 6467-6478
    • Riccardi, D.1    Li, G.H.2    Cui, Q.3
  • 28
    • 70350398133 scopus 로고    scopus 로고
    • High Level QM/MM Modeling of the Formation of the Tetra-hedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A Beta Lactamase
    • Hermann, J. C.; Pradon, J.; Harvey, J. N.; Mulholland, A. J. High Level QM/MM Modeling of the Formation of the Tetra-hedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A Beta Lactamase. J. Phys. Chem. A 2009, 113,11984-11994.
    • (2009) J. Phys. Chem. A , vol.113 , pp. 11984-11994
    • Hermann, J.C.1    Pradon, J.2    Harvey, J.N.3    Mulholland, A.J.4
  • 29
    • 77956890234 scopus 로고
    • Monte-Carlo Sampling Methods Using Markov Chains and Their Applications
    • Hastings, W. K. Monte-Carlo Sampling Methods Using Markov Chains and Their Applications. Biometrika 1970, 57,97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 30
    • 0346350789 scopus 로고    scopus 로고
    • The Development of Replica-Exchange-Based Free-Energy Methods
    • Woods, C. J.; Essex, J. W.; King, M. A. The Development of Replica-Exchange-Based Free-Energy Methods. J. Phys. Chem. B 2003, 107,13703-13710.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 13703-13710
    • Woods, C.J.1    Essex, J.W.2    King, M.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.