Thermochemistry of aqueous solutions of alkylated nucleic acid bases V. Enthalpies of hydration of N-methylated adenines

Zielenkiewicz, A.; Zielenkiewicz, W.; Sukhodub, L. F.; Glukhova, O.T.; Teplitsky, A. B.; Wierzchowski, K.L.

doi:10.1007/bf00647691

Cited by 31 publications

(16 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…That is the reason for investigations of the enthalpy of solvation and evaluation of the energy of interaction of the base molecule with water. The method chosen (1,2) was to screen the functional groups of the skeleton of purine or pyrimidine base by methyl groups to determine the effect of the removal of certain polar and apolar atoms of the skeleton from direct interaction with the hydration shell. The enthalpies of hydration of differently methylated derivatives of uracil and adenine, obtained from experimentally determined enthalpies of solution and enthalpies of sublimation, showed (1,3,4) that methyl groups can be used as thermochemical probes of the molecular potential of water binding around the skeleton of the base.…”

Section: Introductionmentioning

confidence: 99%

“…The method chosen (1,2) was to screen the functional groups of the skeleton of purine or pyrimidine base by methyl groups to determine the effect of the removal of certain polar and apolar atoms of the skeleton from direct interaction with the hydration shell. The enthalpies of hydration of differently methylated derivatives of uracil and adenine, obtained from experimentally determined enthalpies of solution and enthalpies of sublimation, showed (1,3,4) that methyl groups can be used as thermochemical probes of the molecular potential of water binding around the skeleton of the base. It was also stated, that in most cases the elongation of an alkyl side chain by substitution of hydrogen atoms of the skeleton by ethyl, propyl, or butyl groups caused erratic changes of the enthalpy of sublimation and the enthalpy of hydration.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Vapour pressures and molar enthalpies of sublimation for 5-alkyl derivatives of 1,3-dimethyluracil

ński

Zielenkiewicz

1996

The Journal of Chemical Thermodynamics

Self Cite

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Vapour pressures and molar enthalpies of sublimation for 5-alkyl derivatives of 1,3-dimethyluracil

ński

Zielenkiewicz

1996

The Journal of Chemical Thermodynamics

Self Cite

View full text Add to dashboard Cite

“…Experimental data for DNA components are available for quantitative testing of computational methods. These data include interaction energies of individual water molecules with the bases and their derivatives deduced from mass-spectrometric studies (12) and energies of base hydration calculated as the difference of dissolution and sublimation energies of a corresponding substance (13,14).…”

Section: Introductionmentioning

confidence: 99%

Modeling DNA Hydration: Comparison of Calculated and Experimental Hydration Properties of Nuclic Acid Bases

Poltev¹,

Маленков

Gonzalez³

et al. 1996

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

Hydration properties of individual nucleic acid bases were calculated and compared with the available experimental data. Three sets of classical potential functions (PF) used in simulations of nucleic acid hydration were juxtaposed: (i) the PF developed by Poltev and Malenkov (PM), (ii) the PF of Weiner and Kollman (WK), which together with Jorgensen's TIP3P water model are widely used in the AMBER program, and (iii) OPLS (optimized potentials for liquid simulations) developed by Jorgensen (J). The global minima of interaction energy of single water molecules with all the natural nucleic acid bases correspond to the formation of two water-base hydrogen bonds (water bridging of two hydrophilic atoms of the base). The energy values of these minima calculated via PM potentials are in somewhat better conformity with mass-spectrometric data than the values calculated via WK PF. OPLS gave much weaker water-base interactions for all compounds considered, thus these PF were not used in further computations. Monte Carlo simulations of the hydration of 9-methyladenine, 1-methyluracil and 1-methylthymine were performed in systems with 400 water molecules and periodic boundary conditions. Results of simulations with PM potentials give better agreement with experimental data on hydration energies than WK PF. Computations with PM PF of the hydration energy of keto and enol tautomers of 9-methylguanine can account for the shift in the tautomeric equilibrium of guanine in aqueous media to a dominance of the keto form in spite of nearly equal intrinsic stability of keto and enol tautomers. The results of guanine hydration computations are discussed in relation to mechanisms of base mispairing errors in nucleic acid biosynthesis. The data presented in this paper along with previous results on simulation of hydration shell structures in DNA duplex grooves provide ample evidence for the advantages of PM PF in studies of nucleic-acid hydration.

show abstract

“…From this point of view, the recent experimental works devoted to a study of hydration of nucleotide bases and their alkylderivatives (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11) are of certain interest. This problem is most thoroughly studied for Ura, Thy and their alkylderivatives (1,2,(4)(5)(6)(8)(9)(10)(11).…”

Section: Introductionmentioning

confidence: 99%

Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation

Danilov¹,

Tolokh²

1990

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

The simulation performed shows that under methylation of uracil and thymine NH-groups the interaction energy between a base and water (Uwb) is increased. It is also detected that the increase in this energy was observed in the 1st and the 3rd sectors. These conclusions do not confirm the assumption made in the literature on the character of an interaction between methylated bases and water. According to this assumption, when the NH-groups are methylated, the energy of Uwb in these sectors decreases as a result of the van der Waals interactions between a methyl group and water, whose energy compensates the increase in the Uwb energy due to the breaking of an H-bond. Regularity of water molecules near a hydrophobic group under the hydration of polar molecules is detected for the first time.

show abstract

Thermochemistry of aqueous solutions of alkylated nucleic acid bases V. Enthalpies of hydration of N-methylated adenines

Cited by 31 publications

References 16 publications

Vapour pressures and molar enthalpies of sublimation for 5-alkyl derivatives of 1,3-dimethyluracil

Vapour pressures and molar enthalpies of sublimation for 5-alkyl derivatives of 1,3-dimethyluracil

Modeling DNA Hydration: Comparison of Calculated and Experimental Hydration Properties of Nuclic Acid Bases

Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation

Contact Info

Product

Resources

About