New acetamide derivatives containing (ω-p-bromophenoxyalkyl)uracil moiety and their anticytomegalovirus activity

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Photochemical approach to probing different DNA structures

The various conformations of DNA--the A, B, and Z forms, the protein-induced DNA kink, and the G-quartet form--are thought to play important biological roles in processes such as DNA replication, gene expression and regulation, and the repair of DNA damage. The investigation of local DNA conformational changes associated with biological events is therefore essential for understanding the function of DNA. In this Minireview, we discuss the use of photochemical dehalogenation of 5-halouracil-containing DNA to probe the structure of DNA. Hydrogen abstraction by the resultant uracil-5-yl radicals is atom-specific and highly dependent on the structure of the DNA, suggesting that this photochemical approach could be applied as a probe of DNA conformations in living cells.     

Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 48 hydrogen‐bonded amide–thymine and amide–uracil dimers are evaluated from the analytic potential energy function established in our lab recently. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the BSSE correction. For all the 48 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 46 dimers, only two differences are larger than 0.50 kcal/mol and the largest one is only 0.60 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.050 Å for all the 48 dimers. The analytic potential energy function is further applied to four more complicated hydrogen‐bonded amide–base systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded amide–base dimers quickly and accurately. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Gas‐phase hydration of Mg2+ complexes with deprotonated uracil,thymine, uridine,and thymidine

The gas‐phase hydration of Mg²⁺ complexes with deprotonated uracil ( U ), thymine ( T ), uridine ( U _r , uracil riboside), and thymidine ( T _dr , thymine deoxyriboside) was studied. The aim of the work was to analyze the hydration of product ions (eg, [2 U ‐H+Mg]⁺) formed as a result of the collision induced dissociation of the respective parent ion (eg, [3 U _r ‐H+Mg]⁺). The efficiency of gas‐phase hydration of the ions [2 U ‐H+Mg]⁺ and [2 T ‐H+Mg]⁺ was similar. However, the efficiency of gas‐phase hydration of the ion [ U + U _r ‐H+Mg]⁺ was much higher than that of gas‐phase hydration of the ion [ T + T _dr ‐H+Mg]⁺. On the basis of the mass spectra obtained and the performed molecular modelling, it was concluded that in the ion [ T + T _dr ‐H+Mg]⁺, we deal with a steric hindrance due to the presence of a sugar moiety, which affects water attachment. In the ion [ U + U _r ‐H+Mg]⁺, the position of the sugar moiety does not affect water attachment.     

Substituent effect of halogen (F, Cl and Br) on uracil tetrad: A theoretical study

In this paper, the substituted uracil tetrad XU4 (X=F, Cl and Br) where X replace the H atoms at five sites of uracils have been investigated using density functional theory method. Geometries, energies and electrostatic potential energy surfaces have been discussed in detail. The outcomes show that when XU take place of U, the preferred symmetry of the tetrad changed from C₄ to S₄. Stabilization energies indicate that the XU substituted tetrads becomes more and more unstable as from F to Br. ESP maps suggest that U4 could bind a cation while XU4 could not. All the tetrads adopt a nonplanar structure that is not suitable for stacking.     

Thermal Studies on Solid Complexes of Uracil With Some Divalent Transition Metal Ions

The thermal behaviour of Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Pd(II) complexes of uracil was studied by TG, DTG and DTA in a dynamic nitrogen atmosphere. Two processes occur in the isolated uracil complexes: dehydration and pyrolytic decomposition. In the hydrated complexes, the first stage observed was the loss of water molecules, which was followed by decomposition of the uracil. The thermal dehydration of the complexes occurred in from one to three steps. The final decomposition products were found to be the respective metal oxides, except in the cases of the Co(II) and Pd(II) complexes, which produced metallic cobalt and palladium, respectively. The order of reaction and energy of activation for the dehydration stage were evaluated.This revised version was published online in November 2005 with corrections to the Cover Date.     

A novel method for introducing a polyfluoroalkyl group into aromatic compounds

Introduction of a polyfluoroalkyl group into aromatic compounds was achieved by Friedel-Crafts reaction using (1-chloro-1-hydroperfluoroalkyl) sulfides 1, and the subsequent desulfurizing-difluorination of the resulting product using IF₅/Et₃N-nHF. Perfluoroethyl, 1,1,2,2,3,3-hexafluoropropyl, and 1,1,2,2,3,3,4,4,5,5-decafluoropentyl groups were introduced to various aromatic compounds by this method. Selective perfluoroethylation of uracil at the 5-position was also performed.     

Formation of complexes between uracil and calcium ions: an ESI/MS/MS study in combination with theoretical calculations

Cationized uracil clusters around calcium metal ions were generated in the gas phase by electrospray ionization (ESI). A previous study showed that with particular experimental conditions, hexamer, octamer, decamer, dodecamer and tetradecamer uracil clusters are present in high quantities. New experiments were carried out to understand the reasons for the particular stability of these complexes. MS/MS experiments suggested that these uracil clusters belong to the same family. Based on ab initio and DFT quantum chemistry calculations, structures in agreement with experimental results are proposed for these clusters. Copyright © 2009 John Wiley & Sons, Ltd.     

Phenyliodonium Derivatives of N-Heterocycles and CH-Acids, Their Synthesis, and Their Use in the Chemistry of Heterocycles. (Review)

The reactions of iodosylbenzene with CH-acids, including -dicarbonyl and N-heterocyclic compounds in the presence of alkali, which lead to the aryliodonium ylides (betaines) used in the synthesis of new derivatives of heterocycles, are examined. Both -dicarbonyl compounds and the anions of various heterocyclic compounds (pyrrole, indole, pyrazolidinedione, hydroxypyrones, hydroxypyridones, oxo- and dioxopyrimidines) and -keto sulfones, -disulfones, cyclopentadienes, and malononitrile enter into the reaction.     

Synthesis,characterization, and crystal structure of 1,3,7,9-tetramethylpyrido-[2,3-d∶6,5-d′]-dipyrimidine-2,4,6,8-tetrone

A new and easy method for the preparation of 1,3,7,9-tetramethylpyrido-[2,3-d6,5-d]-dipyrimidine-2,4,6,8-tetrone is described. The structure of this compound has been solved by means of X-ray diffraction methods. The chemical characterization by spectral (mass, ultraviolet, infrared, and proton nuclear magnetic resonance) and thermal (thermogravimetry and differential scanning calorimetry) method is also reported. The compound is monoclinic, space groupP2₁/c,a=12.720(5),b=13.688(7),c=8.079(2) Å, =107.06(4)°,Z=4. The structure consists of discrete tricyclic molecules, stacking playing an important role in crystal packing.