Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches

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Title:Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches
Creators:
Fanfrlík, Jindřich
Rejnek, Jaroslav
Hanus, Michal
Hobza, Pavel
Journal or Publication Title:
Collection of Czechoslovak Chemical Communications, 70, 11, pp. 1756-1768
Uncontrolled Keywords:Molecular dynamics, Tautomerism, Pyrimidines, Purines, Hybrid model, Thermodynamic integration, COSMO, Gibbs energy, Nucleobases tautomers, Hydration

Abstract

The hydration Gibbs energies of adenine, cytosine, guanine, thymine, uracil and isoguanine are determined by the molecular dynamics-thermodynamic integration method (MD-TI) and using continuous COSMO and hybrid models. The role of solvents in the COSMO model is described by permittivity and by combining the permittivity and specific hydration of single water molecules placed on the energetically most probable position in the hybrid model. The hybrid model describes hydration similarly to the COSMO model; both the continuous methods are in good agreement with the MD-TI method. Differences are small and the use of both models can be recommended. <p>

Title:Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches
Creators:
Fanfrlík, Jindřich
Rejnek, Jaroslav
Hanus, Michal
Hobza, Pavel
Uncontrolled Keywords:Molecular dynamics, Tautomerism, Pyrimidines, Purines, Hybrid model, Thermodynamic integration, COSMO, Gibbs energy, Nucleobases tautomers, Hydration
Divisions:Life and Chemical Sciences > Institute of Organic Chemistry and Biochemistry > Collection of Czechoslovak Chemical Communications
Journal or Publication Title:Collection of Czechoslovak Chemical Communications
Volume:70
Number:11
Page Range:pp. 1756-1768
ISSN:0010-0765
E-ISSN:1212-6950
Publisher:Institute of Organic Chemistry and Biochemistry
Related URLs:
URLURL Type
http://dx.doi.org/10.1135/cccc20051756UNSPECIFIED
ID Code:2437
Item Type:Article
Deposited On:06 Feb 2009 17:18
Last Modified:06 Feb 2009 16:18

Citation

Fanfrlík, Jindřich; Rejnek, Jaroslav; Hanus, Michal; Hobza, Pavel (2005) Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches. Collection of Czechoslovak Chemical Communications, 70 (11). pp. 1756-1768. ISSN 0010-0765

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