Analyses of the partition coefficient, log P, using ab initio MO parameter and accessible surface area of solute molecules

Chuman, Hiroshi; Mori, Atsushi; Tanaka, Hideji; Yamagami, Chisako; Fujita, Toshio

doi:10.1002/jps.20168

Cited by 25 publications

(24 citation statements)

References 30 publications

(47 reference statements)

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“…Recently, Chuman et al110 directly estimated electrostatic solvation energy using ab initio MO‐Self Consistent Reaction Field (SCRF) calculations within the COSMO model 104. Molecular geometry was optimized in each solvent phase using the Hartree–Fock (HF) calculation at the 3–21G* level.…”

Section: Property‐based Methodsmentioning

confidence: 99%

Calculation of Molecular Lipophilicity: State-of-the-Art and Comparison of LogP Methods on more than 96,000 Compounds

Mannhold

Poda

Ostermann³

et al. 2009

Journal of Pharmaceutical Sciences

572

474

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Section: Property‐based Methodsmentioning

confidence: 99%

Calculation of Molecular Lipophilicity: State-of-the-Art and Comparison of LogP Methods on more than 96,000 Compounds

Mannhold

Poda

Ostermann³

et al. 2009

Journal of Pharmaceutical Sciences

572

474

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“…DASA has been assumed to contain both entropic and enthalpic parts of the hydrophobic interaction energy [52,53]. The other entropic contributions to the free energy change are now considered to be nearly proportional to DE ligand or constant, because the compounds selected for this study consist of a congeneric series.…”

Section: à3mentioning

confidence: 99%

“…The water Accessible Surface Area (ASA) [51], which has often been utilized as a quantitative descriptor that represents the hydrophobic interaction energy [52,53], was calculated with a water probe radius of 1.4 and Bondis van der Waals atomic radii [54] for each element. DASA was defined as follows:…”

Section: Hydrophobic Interactionmentioning

confidence: 99%

QSAR Study of Cyclic Urea Type HIV‐1 PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV‐1 PR

2008

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A quantitative structure-activity relationship study was carried out on a series of cyclic urea type HIV-1 protease inhibitors. In order to determine the atomic and electronic mechanisms in detail, three-dimensional and electronic descriptors were calculated with the molecular dynamics and ab initio fragment molecular orbital calculation of the whole complex structure of HIV-1 protease with each inhibitor. Two descriptors showing correlation with the inhibitory potency were the total interaction energy and the change in the accessible surface area on complex formation with HIV-1 protease. The major contributions to the total electronic interaction energy were found to be from Asp25/25', Asp30/30' and Ile50/50'. The interaction energy with Asp30/30' was nicely correlated with the total electronic interaction energy and also with the charge transfer from Asp30/30', which is in close contact with the substituted moiety in each inhibitor. As well as the hydrophobic interaction, the charge redistribution among the inhibitor and surrounding residues was suggested to govern the variation in the inhibitory potency. The results obtained in this work can help us to reinterpret the classical QSAR descriptors proposed by Garg et al.

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“…(2), we formulated a semiempirical correlation Eq. (3) for log P sol (sol=chloroform (CL) and 1-octanol (oct)) [11][12][13] : (3) takes a value (a=−0.776) close to the expected one (−1/(2.303RT)=−0.734 at 298 K). However, for hydrogen-bonding donors, that is approximately half of the expected value (∼0.34).…”

Section: Partition Coefficient Log Pmentioning

confidence: 79%

“…A general procedure for the LERE-QSAR analysis consists of two steps: (1) determine a complex structure, usually by carrying out classical molecular mechanics and molecular dynamics calculations repeatedly, and (2) calculate Comparison of observed and calculated log P CL values (chloroform/water). Black, gray and dotted bars represent observed log P CL and calculated ones with CPCM 12) and RISM, 15,16) respectively. 24) and (b) concanavalin A, pea lectin, and lentil lectin with monosaccharides.…”

Section: Formulation Of the Lere-qsar Equationmentioning

confidence: 99%

Revisiting the Hansch–Fujita approach and development of a fundamental QSAR

Hitaoka

Chuman

2013

J. Pestic. Sci.

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This review paper is based on the lecture presented in Kyoto on August 25th, 2012, by one of the authors (HC) in the Memorial Symposium for the 50th Anniversary of the Hansch-Fujita Approach; however, several parts have been added. The current paper contains (I) a formulation of an extended one of the well-known Hansch-Fujita QSAR analysis, but a new promising one (called linear expression by representative energy terms (LERE)-QSAR), which can consider ligand-protein interactions explicitly by using modern molecular calculations on a whole ligand-protein complex, and (II) applications of the LERE-QSAR analysis to several cases.

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Analyses of the partition coefficient, log P, using ab initio MO parameter and accessible surface area of solute molecules

Cited by 25 publications

References 30 publications

Calculation of Molecular Lipophilicity: State-of-the-Art and Comparison of LogP Methods on more than 96,000 Compounds

Calculation of Molecular Lipophilicity: State-of-the-Art and Comparison of LogP Methods on more than 96,000 Compounds

QSAR Study of Cyclic Urea Type HIV‐1 PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV‐1 PR

Revisiting the Hansch–Fujita approach and development of a fundamental QSAR

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