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Volumn 125, Issue 25, 2003, Pages 7678-7688

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Guanine: Surprising stabilization of rare tautomers in aqueous solution

Author keywords

[No Author keywords available]

Indexed keywords

ENTHALPY; FREE ENERGY; HYDROGEN; INTEGRATION; ISOMERS; MOLECULAR VIBRATIONS; NITROGEN COMPOUNDS; SOLUTIONS; SOLVENTS; WATER;

EID: 0038207997     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja034245y     Document Type: Article
Times cited : (199)

References (71)
  • 33
  • 48
    • 0037883817 scopus 로고    scopus 로고
    • Mathematica, Wolfram Research, Inc
    • Mathematica, Wolfram Research, Inc.
  • 49
    • 0038221446 scopus 로고    scopus 로고
    • http://www.gromacs.org/contributions/uploaded_contributions/ambconv.tgz.
  • 60
    • 0038221440 scopus 로고    scopus 로고
    • note
    • The RI-MP2 dipole moments presented in Table 1 differ only slightly (in tenths of D) from the HF/6-31G* ones used in RESP procedure, and, consequently, also from the dipole moments yielded by the empirical potential. This means that the electrostatic term of the empirical force field (dominant among nonbonded terms) is described adequately.
  • 61
    • 0003653899 scopus 로고    scopus 로고
    • Pearson Education: Harlow
    • Comparing the ab initio relative free energies with the empirical potential ones (cf Table 1) we found a dramatic difference and the latter values are much too large. We were aware of this problem and we presented the gasphase empirical potential relative free energies only to show the convergence of free energy and to estimate the errors bars. Let us further mention that large values of these relative free energies are not an artifact of the code used; the same values were obtained when using the Amber/Gibbs program. The unrealistically large gas-phase free energies are due to two main reasons: first, empirical force field is by definition unable to describe energy changes during a bond creation, annihilation or modification (Leach, A. R. Molecular Modelling, Principles And Applications; Pearson Education: Harlow, 1996; p 194); second, bonded hydrogen atom cannot be described by classical harmonic potential (GROMACS User Manual, version 3.1.1.). The fact that intermolecular free energy changes are often large is known. The solution of the problem mentioned is relatively easy. The values mentioned will cancel when combining different parts of thermodynamic cycle used (Harris, D.; Loew, G. J. Comput. Chem. 1996, 17, 273). Specifically, the intramolecular contribution to the free energy is the same in vacuo and bulk water and is therefore compensated while the remaining contribution (intermolecular one) forms the hydration free energy
    • (1996) Molecular Modelling, Principles and Applications , pp. 194
    • Leach, A.R.1
  • 62
    • 0000283738 scopus 로고    scopus 로고
    • Comparing the ab initio relative free energies with the empirical potential ones (cf Table 1) we found a dramatic difference and the latter values are much too large. We were aware of this problem and we presented the gasphase empirical potential relative free energies only to show the convergence of free energy and to estimate the errors bars. Let us further mention that large values of these relative free energies are not an artifact of the code used; the same values were obtained when using the Amber/Gibbs program. The unrealistically large gas-phase free energies are due to two main reasons: first, empirical force field is by definition unable to describe energy changes during a bond creation, annihilation or modification (Leach, A. R. Molecular Modelling, Principles And Applications; Pearson Education: Harlow, 1996; p 194); second, bonded hydrogen atom cannot be described by classical harmonic potential (GROMACS User Manual, version 3.1.1.). The fact that intermolecular free energy changes are often large is known. The solution of the problem mentioned is relatively easy. The values mentioned will cancel when combining different parts of thermodynamic cycle used (Harris, D.; Loew, G. J. Comput. Chem. 1996, 17, 273). Specifically, the intramolecular contribution to the free energy is the same in vacuo and bulk water and is therefore compensated while the remaining contribution (intermolecular one) forms the hydration free energy
    • (1996) J. Comput. Chem. , vol.17 , pp. 273
    • Harris, D.1    Loew, G.2
  • 69
    • 0038560075 scopus 로고    scopus 로고
    • note
    • We are aware of the fact that the direct comparison of the thermodynamic results from Monte Carlo - Free Energy Perturbation approach (used in ref 18) and our present results based on Molecular Dynamics-Thermodynamic Integration is not straightforward. Because the convergence limit was not determined in ref 18 we believe that our data are therefore more reliable. Higher number of sampling windows as well as larger box used in the present study give additional evidence about reliability of our results.
  • 70
    • 0037545996 scopus 로고    scopus 로고
    • note
    • Favorable relative hydration free energy of (7,9) tautomer can be explained on the basis of large stabilization energy with water environment. This is confirmed by large stabilization energies of this tautomer with one and two water molecules. Situation with (3,7) tautomer is different since this form possess only modest dipole moment (contrary to (7,9) having very large dipole moment) and, therefore, its stabilization energy with one and two water molecules is also modest. To explain large hydration free energy we evaluated the temperature dependence of hydration free energy. From the slope of this dependence we calculated the entropy term. At 298.15 K the following estimate was obtained: ΔH(-4 kcal/mol); TΔS(15.5kcal/ mol). Despite the fact that the error in determining the enthalpy and entropy contributions can be significant we must admit that the leading stabilization term is entropic one. For the sake of comparison, we performed the same calculation also for (7,9) tautomer and here the entropy term was found considerably smaller: ΔH(-24 kcal/mol); TΔS(6.5kcal/mol).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.