Enthalpies of solvation of alkylated uracils in water,nonaqueous and mixed solvents

The enthalpies of solution of uracil and its alkylated derivatives in water, methanol, N,N-dimethylformamide (DMF) and water+DMF mixtures were measured at 25°C. The enthalpies of solvation were determined. The enthalpies of cavity formation, corresponding to the enthalpies of solvent-solvent interactions were calculated and the enthalpies of solute-solvent interactions were obtained. The presence of the alkyl groups was found to have different effects on the enthalpy of interaction depending on the position and size of the substitution. The effect of alkylation at the nonpolar side of the uracil ring was found to arise mostly from the enhancement of the van der Waals interactions. The alkyl substitutions at the polar side resulted also in the removal of the solvent molecules interacting specifically with the polar groups of uracil. The enthalpy of those specific interactions was determined and found to be stronger in methanol and DMF than in water. Enthalpies of solvation in the binary water+DMF solvent were found to depend in a nonlinear way on the solvent composition. The nonlinearities in the water-rich region were found to arise from the decay of the hydrophobic hydration of the solutes with the increasing DMF content. The substitution of two methyl groups caused the uracil molecule to bahave as a predominantly hydrophobic solute. The nonlinearities in the DMF-rich region were found only for those solutes which can form hydrogen bonds with DMF.     

银颗粒表面尿嘧啶分子的SERS实验研究——KCl对尿嘧啶分子吸附状态的影响

利用表面增强喇曼散射(SERS)在灰银胶体系中研究了KCl对尿嘧啶分子吸附状态的影响,并将实验结果与Oh等人在黄银胶体系中的实验结果进行了详细比较.对这一实验现象进行了定性解释.     

Electrochemical synthesis of 6-amino-5-(3,4-dihydroxyphenyl) pyrimidine

Electrochemical oxidation of several catechols is studied in the presence of 4(6)-aminouracil (3a) and 6-amino-1,3-dimethyl uracil (3b) as nucleophiles in aqueous solution using cyclic voltammetry and controlled-potential coulometry. The results reveal that quinones derived from catechols participate in Michael additions with 3a and 3b to give the corresponding catecholamine derivatives via an electron transfer followed by chemical reaction (EC) mechanistic pathway in good yields and purities.     

Solvation Structure of Uracil in Ionic Liquids

The local solvation environment of uracil dissolved in the ionic liquid 1‐ethyl‐3‐methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute (ionic liquid:uracil) ratios of 3:1 and 2:1, little perturbation of the ion–ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia‐Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109–4120 ). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favourable uracil–uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution.     

Structures of [M(Ura‐H)(H2O)n]+ (M = Mg,Ca, Sr,Ba; n = 1–3) complexes in the gas phase by IRMPD spectroscopy and theoretical studies

The structures of singly and doubly (and for Mg, triply) hydrated group 2 metal dications bound to deprotonated uracil were explored in the gas phase using infrared multiple photon dissociation spectroscopy in the mid‐infrared region (1000–1900 cm^?1) and the O–H/N–H stretching region (2700–3800 cm^?1) in a Fourier transform ion cyclotron resonance mass spectrometer. The infrared multiple photon dissociation spectra were then compared with the computed IR spectra for various isomers. Calculations were performed using B3LYP with the 6‐31 + G(d,p) basis set for all atoms except Ba²⁺ and Sr²⁺, for which the LANL2DZ or the def2‐TZVPP basis sets with relativistic core potentials were used. Atoms‐in‐molecules analysis was conducted for all lowest energy structures. The lowest energy isomers in all cases are those in which the one uracil is deprotonated at the N3 position, and the metal is coordinated to the N3 and O4 of uracil. Regardless of the degree of solvation, all water molecules are bound to the metal ion and participate in a hydrogen bond with a carbonyl of the uracil moiety. Copyright © 2016 John Wiley & Sons, Ltd.     

Nature of ultraviolet and Gamma ray induced damage in crystalline Uracil

Abstract

A study has been made of the damage producedin situ in dry polycrystalline uracil by irradiation with high energy 60Co photons and by low energy ultraviolet (UV) photons. The techniques of electron spin resonance, thin layer chromatography, infrared spectrometry, neutron diffraction and spectrophotometry have all been utilized to investigate effects produced by the irradiations. If was found that little lattice damage and no cis-syn cyclobutane dimers are producedin situ by irradiation of dry uracil with 60Co photons. However, following dissolution of the irradiated powder in water, radiation products are detected, and several of their characteristics have been elucidated. In contrast, following irradiation by 60Co photons of uracil in an aqueous environment, massive damage was found in the dried sample. Irradiation of dry uracil with UV photons is found to cause general lattice damage, but again negligible concentrations of cis-syn dimers are producedin situ. There is evidence for the formation of a planar, dimer-like molecular configuration.     

Cytosine to uracil conversion through hydrolytic deamination of cytidine monophosphate hydroxy‐alkylated on the amino group: a liquid chromatography – electrospray ionization – mass spectrometry investigation

A novel pathway for cytosine to uracil conversion performed in a micellar environment, leading to the generation of uridine monophosphate (UMP), was evidenced during the alkylation reaction of cytidine monophosphate (CMP) by dodecyl epoxide. Liquid chromatography‐electrospray ionization – ion trap ‐ mass spectrometry was used to separate and identify the reaction products and to follow their formation over time. The detection of hydroxy‐amino‐dodecane, concurrently with free UMP, in the reaction mixture suggested that, among the various alkyl‐derivatives formed, CMP alkylated on the amino group of cytosine could undergo tautomerization to an imine and hydrolytic deamination, generating UMP. Interestingly, no evidence for this peculiar conversion pathway was obtained when guanosine monophosphate (GMP), the complementary ribonucleotide of CMP, was also present in the reaction mixture, due to the fact that NH₂‐alkylated CMP was not formed in this case. The last finding emphasized the role played by CMP–GMP molecular interactions, mediated by a micellar environment, in hindering the alkylation reaction at the level of the cytosine amino group. Copyright © 2012 John Wiley & Sons, Ltd.     

DNA base stacking: The stacked uracil/uracil and thymine/thymine minima

The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)‐corrected M06‐2X/6‐31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4‐dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center‐of‐mass, whereas the other monomer remained still. Both face‐to‐back (one molecule exactly on top of the other) and face‐to‐face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas‐phase M06‐2X/6‐31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies. © 2012 Wiley Periodicals, Inc.     

Rare Tautomers of 1‐Methyluracil and 1‐Methylthymine: Tuning Relative Stabilities through Coordination to PtII Complexes

We have computationally explored how the relative stabilities of 1‐methyluracil (1‐MeUH) tautomers can be tuned through coordination of these tautomers to Pt^II complexes with a particular set of ligands. This has been done using density functional theory at the BP86/TZ2P level. Thus, we have examined the water/1‐MeUH exchange reactions of [Pt^II(A)(B)(C)(OH₂)]^q + 1‐MeUH to uncover: i) which tautomers are best stabilized by the Pt^II complex, and ii) how the net charge q in the complex affects the reaction energy. The net charge q depends on the ligands A, B, and C, which can be the neutral NH₃ or anionic Cl^?. To reveal the effect of solvation, all reaction systems are studied both in the gas phase and in water. Also the stabilization of tautomers of 1‐methylthymine (1‐MeTH) by cisplatin is investigated. The calculations reveal that relative energies of the metal (here: Pt^II)‐complexed forms of the various tautomers (here: of 1‐MeUH and 1‐MeTH) do not parallel those of the free tautomers. Rather, a rare nucleobase tautomer, despite its low natural abundance, may become favored over the predominant one when complexed to a metal ion.