Literature DB >> 1291630

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution.

C J Cramer1, D G Truhlar.   

Abstract

Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incorporation of phosphorus parameters, both of these new models address specific deficiencies in the original Solvation Model 1 (AM1-SM1), viz., (1) more accurate account is taken of the hydrophobic effect of hydrocarbons, (2) assignment of heavy-atom surface tensions is based on the presence or absence of bonded hydrogen atoms, and (3) the treatment of specific hydration-shell water molecules is more consistent. The new models offer considerably improved performance compared to AM1-SM1 for neutral molecules and essentially equivalent performance for ions. The solute charges within the Parameterized Model 3 Hamiltonian limit the utility of PM3-SM3 for compounds containing nitrogen and possibly phosphorus. For other systems both AM1-SM2 and PM3-SM3 give realistic results, but AM1-SM2 in general outperforms PM3-SM3. Key features of the models are discussed with respect to alternative approaches.

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Year:  1992        PMID: 1291630     DOI: 10.1007/bf00126219

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  12 in total

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Authors:  C J Cramer; D G Truhlar
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Review 3.  MOPAC: a semiempirical molecular orbital program.

Authors:  J J Stewart
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5.  Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

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Journal:  Proc Natl Acad Sci U S A       Date:  1987-05       Impact factor: 11.205

6.  "Squiggle-H2O". An enquiry into the importance of solvation effects in phosphate ester and anhydride reactions.

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7.  Solvation energy in protein folding and binding.

Authors:  D Eisenberg; A D McLachlan
Journal:  Nature       Date:  1986 Jan 16-22       Impact factor: 49.962

8.  Hydrophobicity of amino acid residues in globular proteins.

Authors:  G D Rose; A R Geselowitz; G J Lesser; R H Lee; M H Zehfus
Journal:  Science       Date:  1985-08-30       Impact factor: 47.728

9.  Interaction of the peptide bond with solvent water: a vapor phase analysis.

Authors:  R Wolfenden
Journal:  Biochemistry       Date:  1978-01-10       Impact factor: 3.162

10.  Empirical correlation between hydrophobic free energy and aqueous cavity surface area.

Authors:  J A Reynolds; D B Gilbert; C Tanford
Journal:  Proc Natl Acad Sci U S A       Date:  1974-08       Impact factor: 11.205

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  23 in total

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7.  Tautomerism of xanthine and alloxanthine: a model for substrate recognition by xanthine oxidase.

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8.  A Monte Carlo method for finding important ligand fragments from receptor data.

Authors:  S Burt; C Hutchins; P J Zielinski
Journal:  J Comput Aided Mol Des       Date:  1997-05       Impact factor: 3.686

9.  Class IV charge models: a new semiempirical approach in quantum chemistry.

Authors:  J W Storer; D J Giesen; C J Cramer; D G Truhlar
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10.  Investigation of catalysis by bacterial RNase P via LNA and other modifications at the scissile phosphodiester.

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