메뉴 건너뛰기




Volumn 58, Issue 6, 2012, Pages 1929-1938

Prediction of the n-hexane/water and 1-octanol/water partition coefficients for environmentally relevant compounds using molecular simulation

Author keywords

[No Author keywords available]

Indexed keywords

AVERAGE ABSOLUTE DEVIATION; CHEMICAL SYSTEMS; DIFFERENT SOLVENTS; EXPERIMENTAL DATA; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; N-HEXANE; PARTITION COEFFICIENT; POLYCHLORINATED BIPHENYL (PCBS); POLYCHLORINATED DIPHENYL ETHERS; PRIORI KNOWLEDGE; THERMODYNAMIC INTEGRATION;

EID: 84860624605     PISSN: 00011541     EISSN: 15475905     Source Type: Journal    
DOI: 10.1002/aic.12718     Document Type: Article
Times cited : (46)

References (77)
  • 1
    • 8644243613 scopus 로고
    • Partition coefficients and their uses
    • Leo A, Hansch C, Elkins D. Partition coefficients and their uses. Chem Rev. 1971; 71( 6): 525-616.
    • (1971) Chem Rev. , vol.71 , Issue.6 , pp. 525-616
    • Leo, A.1    Hansch, C.2    Elkins, D.3
  • 2
    • 0007818845 scopus 로고
    • Investigation of structure, dynamics and solvation in 1-octanol and its water-saturated solution: molecular dynamics and free-energy perturbation studies
    • Debolt SE, Kollman PA. Investigation of structure, dynamics and solvation in 1-octanol and its water-saturated solution: molecular dynamics and free-energy perturbation studies. J Am Chem Soc. 1995; 117( 19): 5316-5340.
    • (1995) J Am Chem Soc. , vol.117 , Issue.19 , pp. 5316-5340
    • Debolt, S.E.1    Kollman, P.A.2
  • 3
    • 33644902649 scopus 로고    scopus 로고
    • Microscopic structure and solvation in dry and wet octanol
    • Chen B, Siepmann JI. Microscopic structure and solvation in dry and wet octanol. J Phys Chem B. 2006; 110( 8): 3555-3563.
    • (2006) J Phys Chem B. , vol.110 , Issue.8 , pp. 3555-3563
    • Chen, B.1    Siepmann, J.I.2
  • 6
    • 66049089399 scopus 로고    scopus 로고
    • Solubility in Food, Pharmaceuticals, and Cosmetic Industries
    • Letcher TM, ed. Cambridge: Royal Society of Chemistry
    • Pinho SP, Macedo EA. Solubility in Food, Pharmaceuticals, and Cosmetic Industries. in: Developments and Applications in Solubility. Letcher TM, ed. Cambridge: Royal Society of Chemistry; 2003: 309-326.
    • (2003) Developments and Applications in Solubility , pp. 309-326
    • Pinho, S.P.1    Macedo, E.A.2
  • 8
    • 0017489826 scopus 로고
    • Partition coefficient and bioaccumulation of selected organic chemicals
    • Chiou CT, Freed VH, Schmedding DW, Kohnert RL. Partition coefficient and bioaccumulation of selected organic chemicals. Environ Sci Techn. 1977; 11( 5): 475-478.
    • (1977) Environ Sci Techn. , vol.11 , Issue.5 , pp. 475-478
    • Chiou, C.T.1    Freed, V.H.2    Schmedding, D.W.3    Kohnert, R.L.4
  • 9
    • 0020128914 scopus 로고
    • Correlation of bioconcentration factors
    • Mackay D. Correlation of bioconcentration factors. Environ. Sci. Techn. 1982; 16( 5): 274-278.
    • (1982) Environ. Sci. Techn. , vol.16 , Issue.5 , pp. 274-278
    • Mackay, D.1
  • 10
    • 0031647914 scopus 로고    scopus 로고
    • Partition coefficients for environmentally important, multifunctional organic compounds in hexane + water
    • Schulte J, Durr J, Ritter S, Hauthal WG, Quittzsch K, Maurer G. Partition coefficients for environmentally important, multifunctional organic compounds in hexane + water. J Chem Eng Data. 1998; 43: 69-73.
    • (1998) J Chem Eng Data , vol.43 , pp. 69-73
    • Schulte, J.1    Durr, J.2    Ritter, S.3    Hauthal, W.G.4    Quittzsch, K.5    Maurer, G.6
  • 11
    • 0036179239 scopus 로고    scopus 로고
    • Experimental and computational screening models for prediction of aqueous drug solubility
    • Bergstrom CAS, Norinder U, Luthman K, Artursson P. Experimental and computational screening models for prediction of aqueous drug solubility. Pharm Res. 2002; 19( 2): 182-188.
    • (2002) Pharm Res. , vol.19 , Issue.2 , pp. 182-188
    • Bergstrom, C.A.S.1    Norinder, U.2    Luthman, K.3    Artursson, P.4
  • 12
    • 12244263506 scopus 로고    scopus 로고
    • Comparison of a miniaturized shake-flask solubility method with automated potentiometric acid/base titrations and calculated solubilities
    • Glomme A, Marz J, Dressman JB. Comparison of a miniaturized shake-flask solubility method with automated potentiometric acid/base titrations and calculated solubilities. J Pharm Sci. 2005; 94( 1): 1-16.
    • (2005) J Pharm Sci. , vol.94 , Issue.1 , pp. 1-16
    • Glomme, A.1    Marz, J.2    Dressman, J.B.3
  • 13
    • 0040914011 scopus 로고
    • ρ-π-σ analysis. A Method for the correlation of biological activity and chemical structure
    • Hansch C, Fujita T. ρ-π-σ analysis. A Method for the correlation of biological activity and chemical structure. J Am Chem Soc. 1964; 86( 8): 1616-1626.
    • (1964) J Am Chem Soc. , vol.86 , Issue.8 , pp. 1616-1626
    • Hansch, C.1    Fujita, T.2
  • 14
    • 24544469216 scopus 로고
    • Calculating log P(Oct) from structures
    • Leo AJ. Calculating log P(Oct) from structures. Chem Rev. 1993; 93( 4): 1281-1306.
    • (1993) Chem Rev. , vol.93 , Issue.4 , pp. 1281-1306
    • Leo, A.J.1
  • 15
    • 0000433140 scopus 로고    scopus 로고
    • Prediction of solvation free energies of small organic molecules: Additive-constitutive models based on molecular fingerprints and atomic constants
    • Viswanadhan VN, Ghose AK, Singh UC, Wendoloski JJ. Prediction of solvation free energies of small organic molecules: Additive-constitutive models based on molecular fingerprints and atomic constants. J Chem Inf Comput Sci. 1999; 39( 2): 405-412.
    • (1999) J Chem Inf Comput Sci. , vol.39 , Issue.2 , pp. 405-412
    • Viswanadhan, V.N.1    Ghose, A.K.2    Singh, U.C.3    Wendoloski, J.J.4
  • 16
    • 39449135396 scopus 로고    scopus 로고
    • The trouble with QSAR (or how i learned to stop worrying and embrace fallacy)
    • Johnson S. The trouble with QSAR (or how i learned to stop worrying and embrace fallacy). J Chem Inf Model. 2008; 48: 25-26.
    • (2008) J Chem Inf Model , vol.48 , pp. 25-26
    • Johnson, S.1
  • 17
    • 0035162354 scopus 로고    scopus 로고
    • Linear free energy relationships used to evaluate equilibrium partitioning of organic compounds
    • Goss K, Schwarzenbach RP. Linear free energy relationships used to evaluate equilibrium partitioning of organic compounds. Environ Sci Techn. 2001; 35( 1): 1-9.
    • (2001) Environ Sci Techn. , vol.35 , Issue.1 , pp. 1-9
    • Goss, K.1    Schwarzenbach, R.P.2
  • 18
    • 13844270669 scopus 로고    scopus 로고
    • Polyparameter linear free energy relationships for estimating the equilibrium partition of organic compounds between water and the natural organic matter in soils and sediments
    • Nguyen TH, Goss K, Ball WP. Polyparameter linear free energy relationships for estimating the equilibrium partition of organic compounds between water and the natural organic matter in soils and sediments. Environ Sci Techn. 2005; 39( 4): 913-924.
    • (2005) Environ Sci Techn. , vol.39 , Issue.4 , pp. 913-924
    • Nguyen, T.H.1    Goss, K.2    Ball, W.P.3
  • 19
    • 0033971341 scopus 로고    scopus 로고
    • The n-octanol and n-hexane/water partition coefficient of environmentally relevant chemicals predicted from the mobile order and disorder (MOD) thermodynamics
    • Ruelle P. The n-octanol and n-hexane/water partition coefficient of environmentally relevant chemicals predicted from the mobile order and disorder (MOD) thermodynamics. Chemosphere. 2000; 40( 5): 457-512.
    • (2000) Chemosphere. , vol.40 , Issue.5 , pp. 457-512
    • Ruelle, P.1
  • 20
    • 0034728673 scopus 로고    scopus 로고
    • Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water
    • Duffy EM, Jorgensen WL. Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water. J Am Chem Soc. 2000; 122( 12): 2878-2888.
    • (2000) J Am Chem Soc. , vol.122 , Issue.12 , pp. 2878-2888
    • Duffy, E.M.1    Jorgensen, W.L.2
  • 21
    • 35948967691 scopus 로고    scopus 로고
    • Refinement of COSMO-SAC and the applications
    • Wang S, Sandler SI, Chen C-C. Refinement of COSMO-SAC and the applications. Ind Eng Chem Res. 2007; 46( 22): 7275-7288.
    • (2007) Ind Eng Chem Res. , vol.46 , Issue.22 , pp. 7275-7288
    • Wang, S.1    Sandler, S.I.2    Chen, C.-C.3
  • 23
    • 0000692122 scopus 로고    scopus 로고
    • Free energy perturbation study of octanol/water partition coefficients: Comparison with continuum GB/SA calculations
    • Best SA, Merz KM, Reynolds CH. Free energy perturbation study of octanol/water partition coefficients: Comparison with continuum GB/SA calculations. J Phys Chem B. 1999; 103( 4): 714-726.
    • (1999) J Phys Chem B. , vol.103 , Issue.4 , pp. 714-726
    • Best, S.A.1    Merz, K.M.2    Reynolds, C.H.3
  • 24
    • 0042943378 scopus 로고
    • Theoretical determination of partition coefficients
    • Essex JW, Reynolds CA, Richards WG. Theoretical determination of partition coefficients. J Am Chem Soc. 1992; 114( 10): 3634-3639.
    • (1992) J Am Chem Soc. , vol.114 , Issue.10 , pp. 3634-3639
    • Essex, J.W.1    Reynolds, C.A.2    Richards, W.G.3
  • 25
    • 0031366060 scopus 로고    scopus 로고
    • Calculation of chloroform/water partition coefficients for the N-methylated nucleic acid bases
    • Eksterowicz JE, Miller JL, Kollman PA. Calculation of chloroform/water partition coefficients for the N-methylated nucleic acid bases. J Phys Chem B. 1997; 101( 50): 10971-10975.
    • (1997) J Phys Chem B. , vol.101 , Issue.50 , pp. 10971-10975
    • Eksterowicz, J.E.1    Miller, J.L.2    Kollman, P.A.3
  • 26
    • 38949113657 scopus 로고    scopus 로고
    • Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations
    • Michel J, Orsi M, Essex JW. Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. J Phys Chem B. 2008; 112( 3): 657-660.
    • (2008) J Phys Chem B. , vol.112 , Issue.3 , pp. 657-660
    • Michel, J.1    Orsi, M.2    Essex, J.W.3
  • 27
    • 79955597262 scopus 로고    scopus 로고
    • Using molecular simulation to predict solvation and partition coefficients in solvents of different polarity
    • Garrido NM, Jorge M, Queimada AJ, Macedo EA, Economou IG. Using molecular simulation to predict solvation and partition coefficients in solvents of different polarity. Phys Chem Chem Phys. 2011; 13: 9155-9164.
    • (2011) Phys Chem Chem Phys , vol.13 , pp. 9155-9164
    • Garrido, N.M.1    Jorge, M.2    Queimada, A.J.3    Macedo, E.A.4    Economou, I.G.5
  • 28
    • 0028235721 scopus 로고
    • Polychlorinated biphenyls (PCBs): Environmental impact, biochemical and toxic responses, and implications for risk assessment
    • Safe SH. Polychlorinated biphenyls (PCBs): Environmental impact, biochemical and toxic responses, and implications for risk assessment. Crit Rev Toxic. 1994; 24( 2): 87-149.
    • (1994) Crit Rev Toxic. , vol.24 , Issue.2 , pp. 87-149
    • Safe, S.H.1
  • 30
    • 77956512551 scopus 로고    scopus 로고
    • Updated abraham solvation parameters for polychlorinated biphenyls
    • van Noort PCM, Haftka JH, Parsons JR. Updated abraham solvation parameters for polychlorinated biphenyls. Environ Sci Technol. 2010; 44: 7037-7042.
    • (2010) Environ Sci Technol , vol.44 , pp. 7037-7042
    • van Noort, P.C.M.1    Haftka, J.H.2    Parsons, J.R.3
  • 31
    • 59249098003 scopus 로고    scopus 로고
    • Estimation of amorphous organic carbon/water partition coefficients, subcooled liquid aqueous solubilities, and n-octanol/water partition coefficients of nonpolar chlorinated aromatic compounds from chlorine fragment constants
    • van Noort PCM. Estimation of amorphous organic carbon/water partition coefficients, subcooled liquid aqueous solubilities, and n-octanol/water partition coefficients of nonpolar chlorinated aromatic compounds from chlorine fragment constants. Chemosphere. 2009; 74: 1024-1030.
    • (2009) Chemosphere , vol.74 , pp. 1024-1030
    • van Noort, P.C.M.1
  • 32
    • 34547841352 scopus 로고    scopus 로고
    • QSPR prediction of n-octanol/water partition coefficient for polychlorinated biphenyls
    • Lu W, Chen Y, Liu M, Chen X, Hu Z. QSPR prediction of n-octanol/water partition coefficient for polychlorinated biphenyls. Chemosphere. 2007; 69( 3): 469-478.
    • (2007) Chemosphere. , vol.69 , Issue.3 , pp. 469-478
    • Lu, W.1    Chen, Y.2    Liu, M.3    Chen, X.4    Hu, Z.5
  • 33
    • 77953809652 scopus 로고    scopus 로고
    • QSPR/QSAR models for prediction of the physico-chemical properties and biological activity of polychlorinated diphenyl ethers (PCDEs)
    • Hui-Ying X, Jian-Wei Z, Gui-Xiang H, Wei W. QSPR/QSAR models for prediction of the physico-chemical properties and biological activity of polychlorinated diphenyl ethers (PCDEs). Chemosphere. 2010; 80: 665-670.
    • (2010) Chemosphere , vol.80 , pp. 665-670
    • Hui-Ying, X.1    Jian-Wei, Z.2    Gui-Xiang, H.3    Wei, W.4
  • 34
    • 33845279234 scopus 로고
    • Linear solvation energy relationships 46: an improved equation for correlation and prediction of octanol water partition coefficients of organic nonelectrolytes (including strong hydrogen-bond donor solutes)
    • Kamlet MJ, Doherty RM, Abraham MH, Marcus Y, Taft RW. Linear solvation energy relationships 46: an improved equation for correlation and prediction of octanol water partition coefficients of organic nonelectrolytes (including strong hydrogen-bond donor solutes). J Phys Chem. 1988; 92( 18): 5244-5255.
    • (1988) J Phys Chem. , vol.92 , Issue.18 , pp. 5244-5255
    • Kamlet, M.J.1    Doherty, R.M.2    Abraham, M.H.3    Marcus, Y.4    Taft, R.W.5
  • 35
    • 84961979135 scopus 로고    scopus 로고
    • 1-Octanol/water partition coefficients of n-alkanes from molecular simulations of absolute solvation free energies
    • Garrido NM, Queimada AJ, Jorge M, Macedo EA, Economou IG. 1-Octanol/water partition coefficients of n-alkanes from molecular simulations of absolute solvation free energies. J Chem Theory Comput. 2009; 5( 9): 2436-2446.
    • (2009) J Chem Theory Comput. , vol.5 , Issue.9 , pp. 2436-2446
    • Garrido, N.M.1    Queimada, A.J.2    Jorge, M.3    Macedo, E.A.4    Economou, I.G.5
  • 36
    • 33645104033 scopus 로고    scopus 로고
    • Force field evaluation for biomolecular simulation: Free enthalpies of solvation of polar and apolar compounds in various solvents
    • Geerke DP, van Gunsteren WF. Force field evaluation for biomolecular simulation: Free enthalpies of solvation of polar and apolar compounds in various solvents. Chemphyschem. 2006; 7( 3): 671-678.
    • (2006) Chemphyschem. , vol.7 , Issue.3 , pp. 671-678
    • Geerke, D.P.1    van Gunsteren, W.F.2
  • 37
    • 0034641331 scopus 로고    scopus 로고
    • Partitioning of alkane and alcohol solutes between water and (Dry or wet) 1-Octanol
    • Chen B, Siepmann JI. Partitioning of alkane and alcohol solutes between water and (Dry or wet) 1-Octanol. J Am Chem Soc. 2000; 122( 27): 6464-6467.
    • (2000) J Am Chem Soc. , vol.122 , Issue.27 , pp. 6464-6467
    • Chen, B.1    Siepmann, J.I.2
  • 38
    • 77949975511 scopus 로고    scopus 로고
    • Potentials and algorithms for incorporating polarizability in computer simulations
    • Rick SW, Stuart SJ. Potentials and algorithms for incorporating polarizability in computer simulations. Rev Comput Chem. 2002; 18: 89-146.
    • (2002) Rev Comput Chem , vol.18 , pp. 89-146
    • Rick, S.W.1    Stuart, S.J.2
  • 40
    • 0000249851 scopus 로고
    • Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
    • Beuler TM R, van Schaik RC, Gerber PR, van Gunsteren WF. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem Phys Lett. 1994; 222: 529-539.
    • (1994) Chem Phys Lett , vol.222 , pp. 529-539
    • Beuler, T.R.1    van Schaik, R.C.2    Gerber, P.R.3    van Gunsteren, W.F.4
  • 42
    • 77951141262 scopus 로고    scopus 로고
    • The effect of integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration
    • Jorge M, Garrido NM, Queimada AJ, Economou IG, Macedo EA. The effect of integration method on the accuracy and computational efficiency of free energy calculations using thermodynamic integration. J Chem Theory Comput. 2010; 6( 4): 1018-1027.
    • (2010) J Chem Theory Comput. , vol.6 , Issue.4 , pp. 1018-1027
    • Jorge, M.1    Garrido, N.M.2    Queimada, A.J.3    Economou, I.G.4    Macedo, E.A.5
  • 43
    • 0001061046 scopus 로고    scopus 로고
    • Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes
    • Martin MG, Siepmann JI. Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes. J Phys Chem B. 1998; 102( 14): 2569-2577.
    • (1998) J Phys Chem B. , vol.102 , Issue.14 , pp. 2569-2577
    • Martin, M.G.1    Siepmann, J.I.2
  • 44
    • 0000013131 scopus 로고    scopus 로고
    • Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. United-atom description of branched alkanes
    • Martin MG, Siepmann JI. Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. United-atom description of branched alkanes. J Phys Chem B. 1999; 103( 21): 4508-4517.
    • (1999) J Phys Chem B. , vol.103 , Issue.21 , pp. 4508-4517
    • Martin, M.G.1    Siepmann, J.I.2
  • 45
    • 0037134595 scopus 로고    scopus 로고
    • Monte Carlo calculations for alcohols and their mixtures with alkanes. Transferable potentials for phase equilibria. 5. United-atom description of primary, secondary, and tertiary alcohols
    • Chen B, Potoff JJ, Siepmann JI. Monte Carlo calculations for alcohols and their mixtures with alkanes. Transferable potentials for phase equilibria. 5. United-atom description of primary, secondary, and tertiary alcohols. J Phys Chem B. 2001; 105( 15): 3093-3104.
    • (2001) J Phys Chem B. , vol.105 , Issue.15 , pp. 3093-3104
    • Chen, B.1    Potoff, J.J.2    Siepmann, J.I.3
  • 46
    • 9144220288 scopus 로고    scopus 로고
    • Transferable potentials for phase equilibria. 6. United-atom description for ethers, glycols, ketones, and aldehydes
    • Stubbs JM, Potoff JJ, Siepmann JI. Transferable potentials for phase equilibria. 6. United-atom description for ethers, glycols, ketones, and aldehydes. J Phys Chem B. 2004; 108( 45): 17596-17605.
    • (2004) J Phys Chem B. , vol.108 , Issue.45 , pp. 17596-17605
    • Stubbs, J.M.1    Potoff, J.J.2    Siepmann, J.I.3
  • 47
    • 34848823435 scopus 로고    scopus 로고
    • Transferable potentials for phase equilibria. 9. explicit hydrogen description of benzene and five-membered and six-membered heterocyclic aromatic compounds
    • Rai N, Siepmann JI. Transferable potentials for phase equilibria. 9. explicit hydrogen description of benzene and five-membered and six-membered heterocyclic aromatic compounds. J Phys Chem B. 2007; 111: 10790-10799.
    • (2007) J Phys Chem B , vol.111 , pp. 10790-10799
    • Rai, N.1    Siepmann, J.I.2
  • 48
    • 84860601422 scopus 로고    scopus 로고
    • Predicting hydration gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data
    • Submitted for publication.
    • Garrido NM, Jorge M, Queimada AJ, Economou IG, Macedo EA. Predicting hydration gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data. Submitted for publication. 2011.
    • (2011)
    • Garrido, N.M.1    Jorge, M.2    Queimada, A.J.3    Economou, I.G.4    Macedo, E.A.5
  • 49
    • 0032484752 scopus 로고    scopus 로고
    • Engineering a molecular model for water phase equilibrium over a wide temperature range
    • Boulougouris GC, Economou IG, Theodorou DN. Engineering a molecular model for water phase equilibrium over a wide temperature range. J Phys Chem B. 1998; 102( 6): 1029-1035.
    • (1998) J Phys Chem B. , vol.102 , Issue.6 , pp. 1029-1035
    • Boulougouris, G.C.1    Economou, I.G.2    Theodorou, D.N.3
  • 50
    • 7044260905 scopus 로고    scopus 로고
    • Free energies of hydration from a generalized born model and an all-atom force field
    • Jorgensen WL, Ulmschneider JP, Tirado-Rives J. Free energies of hydration from a generalized born model and an all-atom force field. J Phys Chem. B. 2004; 108: 16264-16270.
    • (2004) J Phys Chem. B. , vol.108 , pp. 16264-16270
    • Jorgensen, W.L.1    Ulmschneider, J.P.2    Tirado-Rives, J.3
  • 51
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem. Theory Comput. 2008; 4( 3): 435-447.
    • (2008) J Chem. Theory Comput. , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 52
    • 84943200457 scopus 로고
    • A leap-frog algorithm for stochastic dynamics
    • van Gunsteren W, Berendsen H. A leap-frog algorithm for stochastic dynamics. Mol Sim. 1988; 1( 3): 173-185.
    • (1988) Mol Sim. , vol.1 , Issue.3 , pp. 173-185
    • van Gunsteren, W.1    Berendsen, H.2
  • 53
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess B, Bekker H, Berendsen HJC, Fraaije J. LINCS: A linear constraint solver for molecular simulations. J Comp Chem. 1997; 18( 12): 1463-1472.
    • (1997) J Comp Chem. , vol.18 , Issue.12 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.4
  • 54
    • 84986440341 scopus 로고
    • Settle - an analytical version of the shake and rattle agorithm for rigid water molecules
    • Miyamoto S, Kollman PA. Settle - an analytical version of the shake and rattle agorithm for rigid water molecules. J Comp Chem. 1992; 13( 8): 952-962.
    • (1992) J Comp Chem. , vol.13 , Issue.8 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 56
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee FS, Warshel A. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J Chem Phys. 1992; 97( 5): 3100-3107.
    • (1992) J Chem Phys. , vol.97 , Issue.5 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 57
    • 0141990949 scopus 로고    scopus 로고
    • Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
    • Shirts MR, Pitera JW, Swope WC, Pande VS. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins. J Chem Phys. 2003; 119( 11): 5740-5761.
    • (2003) J Chem Phys. , vol.119 , Issue.11 , pp. 5740-5761
    • Shirts, M.R.1    Pitera, J.W.2    Swope, W.C.3    Pande, V.S.4
  • 58
    • 84906393269 scopus 로고
    • Algorithms for brownian dynamics
    • Van Gunsteren WF, Berendsen HJC. Algorithms for brownian dynamics. Mol Phys. 1982; 45( 3): 637-647.
    • (1982) Mol Phys. , vol.45 , Issue.3 , pp. 637-647
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 60
    • 33646887390 scopus 로고
    • On the limited memory BFGS method for large-scale optimization
    • Liu DC, Nocedal J. On the limited memory BFGS method for large-scale optimization. Math Programm. 1989; 45( 3): 503-528.
    • (1989) Math Programm. , vol.45 , Issue.3 , pp. 503-528
    • Liu, D.C.1    Nocedal, J.2
  • 64
    • 34548703110 scopus 로고    scopus 로고
    • Alchemical free energy calculations: ready for prime time?
    • Shirts MR, Mobley DL, Chodera JD. Alchemical free energy calculations: ready for prime time? Ann Rep Comput Chem. 2007; 3( 4): 41-59.
    • (2007) Ann Rep Comput Chem. , vol.3 , Issue.4 , pp. 41-59
    • Shirts, M.R.1    Mobley, D.L.2    Chodera, J.D.3
  • 65
    • 65249187748 scopus 로고    scopus 로고
    • Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations
    • Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. J Chem Theory Comput. 2009; 5( 2): 350-358.
    • (2009) J Chem Theory Comput. , vol.5 , Issue.2 , pp. 350-358
    • Mobley, D.L.1    Bayly, C.I.2    Cooper, M.D.3    Shirts, M.R.4    Dill, K.A.5
  • 66
    • 0037439922 scopus 로고    scopus 로고
    • Using pc clusters to evaluate the transferability of molecular mechanics force fields for proteins
    • Okur A, Strockbine B, Hornak V, Simmerling C. Using pc clusters to evaluate the transferability of molecular mechanics force fields for proteins. J Comput Chem. 2003; 24: 21-31.
    • (2003) J Comput Chem , vol.24 , pp. 21-31
    • Okur, A.1    Strockbine, B.2    Hornak, V.3    Simmerling, C.4
  • 67
    • 29044442254 scopus 로고    scopus 로고
    • Molecular modeling of organic and biomolecular systems using boss and mcpro
    • Jorgensen WL, Tirado-Rives J. Molecular modeling of organic and biomolecular systems using boss and mcpro. J Comput Chem. 2005; 26( 16): 1689-1700.
    • (2005) J Comput Chem. , vol.26 , Issue.16 , pp. 1689-1700
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 68
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996; 118( 45): 11225-11236.
    • (1996) J Am Chem Soc. , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 69
    • 25644439980 scopus 로고    scopus 로고
    • Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA
    • Price DJ, Brooks IIICL. Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA. J Comput Chem. 2005; 26: 1529-1541.
    • (2005) J Comput Chem , vol.26 , pp. 1529-1541
    • Price, D.J.1    Brooks III, C.L.2
  • 70
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J Comp Chem. 2004; 25( 13): 1656-1676.
    • (2004) J Comp Chem. , vol.25 , Issue.13 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 71
    • 37049082205 scopus 로고
    • A Thermodynamic and solvatochromic investigation of the effect of water on the phase transfer properties of Ocatn-1-ol
    • Dallas AJ, Carr PW. A Thermodynamic and solvatochromic investigation of the effect of water on the phase transfer properties of Ocatn-1-ol. J Chem Soc Perkin Trans 2. 1992( 12): 2155-2161.
    • (1992) J Chem Soc Perkin Trans 2. , Issue.12 , pp. 2155-2161
    • Dallas, A.J.1    Carr, P.W.2
  • 72
    • 0021685194 scopus 로고
    • Accurate, wide-range, automated, high-performance liquid chromatographic method for the estimation of octanol/water partition coefficients I: Effect of chromatographic conditions and procedure variables on accuracy and reproducibility of the method
    • Garst JE, Wilson WC. Accurate, wide-range, automated, high-performance liquid chromatographic method for the estimation of octanol/water partition coefficients I: Effect of chromatographic conditions and procedure variables on accuracy and reproducibility of the method. J Pharm Sci. 1984; 73( 11): 1616-1623.
    • (1984) J Pharm Sci. , vol.73 , Issue.11 , pp. 1616-1623
    • Garst, J.E.1    Wilson, W.C.2
  • 73
    • 0026329516 scopus 로고
    • Chemical topology and ecotoxicology
    • Sabljic A. Chemical topology and ecotoxicology. Sci Total Environ. 1991; 109/110: 197-220.
    • (1991) Sci Total Environ. , vol.109-110 , pp. 197-220
    • Sabljic, A.1
  • 74
    • 0036628547 scopus 로고    scopus 로고
    • Novel methods for the prediction of log P, pKa, and log D
    • Xing L, Glen RC. Novel methods for the prediction of log P, pKa, and log D. J Chem Inf Comput Sci. 2002; 42: 796-805.
    • (2002) J Chem Inf Comput Sci , vol.42 , pp. 796-805
    • Xing, L.1    Glen, R.C.2
  • 75
    • 0028464119 scopus 로고
    • Computer automated log p calculations based on an extended group contribution approach
    • Klopman G, Li J-Y, Wang S, Dimayuga M. Computer automated log p calculations based on an extended group contribution approach. J Chem Inf Comput Sci. 1994; 34: 752-781.
    • (1994) J Chem Inf Comput Sci , vol.34 , pp. 752-781
    • Klopman, G.1    Li, J.-Y.2    Wang, S.3    Dimayuga, M.4
  • 76
    • 0032112162 scopus 로고    scopus 로고
    • Toward a principled methodology for neural network design and performance evaluation in QSAR. Application to the prediction of logp
    • Duprat AF, Huynh T, Dreyfus G. Toward a principled methodology for neural network design and performance evaluation in QSAR. Application to the prediction of logp. J Chem Inf Comput Sci. 1998; 38: 586-594.
    • (1998) J Chem Inf Comput Sci , vol.38 , pp. 586-594
    • Duprat, A.F.1    Huynh, T.2    Dreyfus, G.3
  • 77
    • 0000055756 scopus 로고    scopus 로고
    • QM/NN QSPR models with error estimation: Vapor pressure and logp
    • Beck B, Breindl A, Clark T. QM/NN QSPR models with error estimation: Vapor pressure and logp. J Chem Inf Comput Sci. 2000; 40: 1046-1054.
    • (2000) J Chem Inf Comput Sci , vol.40 , pp. 1046-1054
    • Beck, B.1    Breindl, A.2    Clark, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.