Analysis of dielectric properties of cytosine in aqueous solution

Manzur, María E.; Romano, Élida; Vallejo, Segundo Pablo; Wesler, S.; Suvire, Fernando D.; Enriz, Ricardo D.; Molina, M.A.A.

doi:10.1016/s0167-7322(01)00260-4

Cited by 9 publications

(5 citation statements)

References 19 publications

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“…Table compiles the dipole moments predicted at the B3LYP/DZP++ level for the isolated nucleic acid bases and the 2‘-deoxyribonucleosides. For comparison, available experimental , results are included. Interestingly, the B3LYP/DZP++ dipole moments of the nucleosides (except for dG) exhibit closer agreement with experiment than the isolated nucleic acid bases.…”

Section: Resultsmentioning

confidence: 99%

DNA Nucleosides and Their Radical Anions: Molecular Structures and Electron Affinities

et al. 2004

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The deoxyribonucleosides have been studied to determine the properties of combinations of 2-deoxyribose with each of the isolated DNA bases for both neutral and anionic species. We have used a carefully calibrated theoretical method [Chem. Rev. 2002, 102, 231], employing the B3LYP hybrid Hartree-Fock/DFT functional with the DZP++ basis set. Predictions are made of the geometric parameters, adiabatic electron affinities, charge distributions based on natural population analysis, and decomposition enthalpy for the neutral and anionic forms of the four 2'-deoxyribonucleosides in DNA: 2'-deoxyriboadenosine (dA), 2'-deoxyribocytidine (dC), 2'-deoxyriboguanosine (dG), and 2'-deoxyribothymidine (dT). Geometric changes in the anions show that the glycosidic bond exhibits little change with excess charge for the guanosine but significant shortening for the adenosine and for the pyrimidines. The zero-point corrected adiabatic electron affinities in eV for each of the 2'-deoxyribonucleosides are as follows: 0.06, dA; 0.09, dG; 0.33, dC; and 0.44, dT. These values are uniformly greater than those of the corresponding isolated bases (-0.28, A; -0.07, G; 0.03, C; 0.20, T) and the isolated 2-deoxyribose (-0.38) at the same level of theory. The vertical detachment energies of dT and dC are substantial, 0.72 and 0.94 eV, and these anions should be observable. A high VDE, 0.91 eV, is also found for dA but its anion is unlikely to be stable due to the small AEA of 0.06 eV. The high VDE reflects the fact that the molecular structures of the anions and the corresponding neutral species are quite different. Valence character is displayed for the SOMOs of dA, dC, and dT, while some component of diffuse character is visible in the SOMO of dG. Further analysis of electronic changes upon electron attachment include an examination of the NPA charges, which show that in the neutral 2'-deoxyribonucleosides the sum of NPA charges for every base is the same, -0.28 with the sum of 2-deoxyribose charges being positive, +0.28. In the anions, the trend in charge division varies based on the nature of the excess electron in the anions. Thermodynamically, the overall enthalpy change for the reaction of water with the neutral nucleosides to give bases and ribose is approximately zero. The analogous decomposition is exothermic by 8 to 11 kcal mol-1 for the anions, indicating possible challenges for anionic gas-phase nucleoside exploration in the presence of water.

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Section: Resultsmentioning

confidence: 99%

DNA Nucleosides and Their Radical Anions: Molecular Structures and Electron Affinities

et al. 2004

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“…We used dipole moments measured in benzene at 298K, when available. Dipole moments of imidazole and nucleotides were taken from original experimental studies 88–94 . Theoretically calculated dipole moments were used only for several nucleotide derivatives 57 .…”

Section: Methodsmentioning

confidence: 99%

“…Experimental dipole moments were taken from compilations for molecules and molecular groups. , We used dipole moments measured in benzene at 298 K, when available. Dipole moments of imidazole and nucleotides were taken from original experimental studies. − Theoretically calculated dipole moments were used only for several nucleotide derivatives . The sum of group dipole moments varied from zero to 9.2 D in our data set.…”

Section: Methodsmentioning

confidence: 99%

Anisotropic Solvent Model of the Lipid Bilayer. 1. Parameterization of Long-Range Electrostatics and First Solvation Shell Effects

Lomize

Pogozheva

Mosberg

2011

J. Chem. Inf. Model.

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A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σi) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules, or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σi and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for non-polar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

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“…As one of the nitric bases of nucleic acids, it fulfills the function of data carrier onto which all information is recorded on the structure, metabolism, and vital functions of organisms, their species affiliation, family, and even kingdom. [1][2][3][4][5] Having taken account of the above information, one must note how important it is to conduct research aimed at identifying appropriate substances which could prevent various diseases and prolong organisms' vital functions. Many pathogenic agents undergo mutations and become immune to administered drugs.…”

Section: Introductionmentioning

confidence: 99%

Successful Separation and Determination of Isomers of Cytosine Derivatives for HPLC

Kluska

Prukała

et al. 2014

Journal of Liquid Chromatography & Related Technologies

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& The work presents research results on separation and determination of three isomers: 1-N-o-(m-or p-)bromobenzyl-[5-(4 0 -morpholinyl)methyl]cytosines. The research included three stationary phases and three mobile phases: acetonitrile, methanol, mixture of acetonitrile=water= formic acid. When using octadecyl stationary phase considered to be standard as well as the octyl one, no separation of the aforementioned isomers of cytosine derivatives was observed, regardless of the mobile phase type. It was only when the chemically bonded aryl (naphthylpropyl) stationary phase was used that the separation of the aforementioned isomers was possible within 7 min. This phase was also characterized by the greatest selectivity ( ¼ 1.90 and 1.53) of the cytosine derivatives being assayed, with the use of methanol as the mobile phase at 0.5 mL=min flow.

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Analysis of dielectric properties of cytosine in aqueous solution

Cited by 9 publications

References 19 publications

DNA Nucleosides and Their Radical Anions: Molecular Structures and Electron Affinities

DNA Nucleosides and Their Radical Anions: Molecular Structures and Electron Affinities

Anisotropic Solvent Model of the Lipid Bilayer. 1. Parameterization of Long-Range Electrostatics and First Solvation Shell Effects

Successful Separation and Determination of Isomers of Cytosine Derivatives for HPLC

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