Electrophilic ipso-substitution in uracil derivatives

Treatment of 5-iodo-1,3,6-trimethyluracil with 50% H₂SO₄ gives 1,3,6-trimethyluracil; with 5-bromo-1,3,6-trimethyluracil, a mixture of 1,3,6-trimethyluracil and 6-bromomethyl-1,3-dimethyluracil is obtained. 5-Chloro-1,3,6-trimethyluracil remains inert under these conditions. According to the DFT modeling of the reactions of 5-halo-1,3,6-trimethyluracils, a nucleophilic agent can abstract either Hal⁺ or the methyl proton from the carbocation formed by protonation of the starting halouracil at position 5, which accounts for the formation of two products from the 5-bromo derivative. Under similar conditions, 6-methyluracil dibromohydrin yields N-bromo-5-bromo-6-hydroxymethyluracil. Bromination or chlorination of 5-hydroxymethyl- or 5-formyl-6-methyluracils follows the ipso-substitution scheme leading to 6-methyluracil 5-halo- and 5,5-dihalohydrins.     

Apparent molar heat capacities and volumes of some alkylated derivatives of uracil and adenine in aqueous solution at 25°C

Densities and apparent molar heat capacities of some alkylated derivatives of uracil and adenine: 1-methyluracil, 1,3-dimethyluracil, 1,3-diethylthymine, 5,6-trimethylene-1,3-dimethyluracil, 5,6-tetramethylene-1,3-dimethyluracil, 5,6-pentamethylene-1,3-dimethyluracil, 2,9-dimethyladenine, 2-ethyl-9-methyladenine, 2-propyl-9-methyladenine, 8-ethyl-9-methyladenine, 6,8,9-trimethyladenine and 8-ethyl-6,9-dimethyladenine were determined using flow calorimetry and flow densimetry at 25°C. It was found that the partial molar volumes and heat capacities correlate linearly with the number of substituted methylene groups-CH ₂ -as well as to the number of hydrogen atoms, n _H , belonging to the skeleton of the molecule. In the case of alkylated uracils a difference was observed in the values at infinite dilution V ₂ ^o and C _p2 ^o , depending on the substitution of alkyl and cyclooligomethylene groups.     

The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications

The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have deltaH(acid) values of 331-333 kcal mol(-1); the acidity of the N3 sites fall between 347-352 kcal mol(-1). The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol(-1), and 369 kcal mol(-1) in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol(-1). Calculations conducted at B3LYP/6-31+G* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed.     

Reaction of aromatic aldehydes with β-dicarbonyl compounds in a catalytic system: Piperidinium acetate-1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid

Condensation of aromatic (heteroaromatic) aldehydes with 1,3-dicarbonyl compounds under the 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim][BF₄]) ionic liquid-piperidinium acetate catalytic system (0.2 equiv. of each component) in the absence of a solvent affords, depending on the structures of the reagents, 2-arylidene derivatives of methyl acetoacetate and acetylacetone, diethyl 2,4-bis(trifluoroacetyl)-3-phenylpentanedioate, or dimethyl 2-aryl-4-hydroxy-6-oxocyclohexane-1,3-dicarboxylates. The reactions of the resulting 2-arylidene derivatives with O-methylisourea in the [Bmim][BF₄] ionic liquid produced methyl 2-methoxy-4-methyl-6-aryldihydropyrimidine-5-carboxylates and 1-(2-methoxy-4-methyl-6-phenyldihydropyrimidin-5-yl)ethanone (mixtures of 3,6- and 1,6-dihydro isomers), which were transformed into the corresponding 3,4-dihydropyrimidin-2(1H)-one derivatives. Dedicated to Academician N. K. Kochetkov on the occasion of his 90th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1199–1204, May, 2005.     

Synthesis of acyclic and macrocyclic analogs of Di-, Tri-, and tetranucleotides

Compounds consisting of two or three uracil fragments were synthesized by reaction of methyl-substituted uracil sodium salts with 1-(6-bromohexyl)-3,6-dimethyluracil or 1,6-dibromohexane. Treatment of these compounds with paraformaldehyde gave the corresponding pyrimidinophanes and acyclic compounds in which the uracil fragments are linked through methylene bridges. Uracil derivatives having no substituent on N³ were synthesized by reactions of silylated uracils with 1,3-bis(6-bromohexyl)uracil or 4,4′-(6-bromohexyloxy)diphenylmethane. The acyclic compound was converted into pyrimidinophane containing uracil fragments with N³H groups. A trinucleotide analog including uracil and two adenine fragments was synthesized from 1,3-bis(6-bromohexyl)uracil.     

Research on the pyrimidine series

The reaction of 4-chloro-2-ethylthio-6-methylpyrimidine with 30% H₂O₂ in ethanol with heating forms 5-chloro-6-methyluracil instead of the expected 4-chloro-2-hydroxy-6-methylpyrimidine. Under similar conditions but in the presence of HC1, 6-methyluracil and 2-ethylthio-4-hydroxy-6-methylpyrimidine are also converted into 5-chloro-6-methyluracil.For part IV, see [10].     

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. VIII. Enthalpies of hydration of 6-alkyluracils

Enthalpies of solution in water H _sol ^o and enthalpies of sublimation H _sub ^o were determined for a number of crystalline derivatives of uracil: 1,6-dimethyluracil (m ₂ ^1,6 Ura), 1,3,6-trimethyluracil (m ₃ ^1,3,6 Ura), 6-ethyl-1,3-dimethyluracil (e⁶m ₂ ^1,3 Ura), 6-propyl-1,3-dimethyluracil (pr⁶m ₂ ^1,3 Ura) and 6-butyl-1,3-dimethyluracil (but⁶m ₂ ^1,3 Ura). Standard enthalpies of hydration H _hydr ^o and standard enthalpies of interaction H _int ^o of the solutes with their hydration shells were calculated. The data obtained show that dependence of H _int ^o on the number of-CH₂- groups of n-alkyl chain added upon substitution of diketopyrimidine ring is nonlinear. This finding is discussed in connection with results of X-ray diffraction structure determinations for the crystalline compounds.     

Alkylation of pyrimidine derivatives with ethylene chlorohydrin

Alkylation of 6-methyluracil, 5-fluorouracil, uracil-5-ammonium sulfate, 5-hydroxyuracil, 5-hydroxy-6-methyluracil, 3,6-dimethyl-5-hydroxyuracil, and 1,3,6-trimethyl-5-hydroxyuracil with ethylene chlorohydrin in water-alcohol medium in the presence of KOH was investigated.     

The synthesis and properties of certain N-methylated 5-diazouracils

The reduction of 1-methyl-, 3-methyl- and 1,3-dimethyl-5-nitrouracil (Ia-c) to the corresponding 5-aminouracils (IIa-c) is described. Diazotization of 5-amino-1-methyluracil (IIa) and 5-amino-1,3-dimethyluracil (IIc) gave 5-diazouracils which were characterized as thermally stable C6 covalent hydrates (III and XIII). Diazotization of 5-amino-3-methyluracil (IIb) gave anhydro 5-diazo-3-methyluracil (X) which underwent covalent methanolation and thermally reversible covalent hydration. Treatment of III and XIII with hot methanol resulted in solvent exchange of the C6 hydroxyl groups by a mechanism which may involve initial formation of diazoethers. Treatment of the methanolates (IV, XI and XIV) with dimethylamine resulted in coupling at the diazo group with a concomitant expulsion of the C6 methoxyl groups to give 5-(3,3-dimethyl-1-triazeno)uracils (XVa-c).     

Photochemical reaction of 8-azaxanthine with nucleophiles

Photolysis of 1,3,7-trimethyl-8-azaxanthine $\text{(1)}$ in the presence of primary and secondary alkylamines gave 6-alkylamino-5-methylamino-1,3-dimethyluracils $\text{(2)}$, whereas irradiation of $\text{1}$ in methanol yielded 5-hydroxy-6-methoxy-1,3-dimethyluracil $\text{(3)}$.     

Synthesis and Structure of New Substituted Pyrimidinone with Unsaturated Side Chain

Melting of a mixture of 5-substituted 2,4-dimethyl-1,6-dihydropyrimidin-6-ones with cinnamic aldehyde, 1-methylindoline-2,3-dione and 6-methoxy-2-chloroquinoline-3-carbaldehyde in the presence of ZnCl₂ led to the formation of substituted pyrimidines with conjugated bonds in the position 2. The structure of synthesized compounds as 2-isomers was confirmed by 2D ¹H NMR NOESY data.     

1,3-二(乙氧基甲基)-5-N,N-二甲氨基-6-甲基尿嘧啶的合成

报道了1,3-二(乙氧基甲基)-5-N,N-二甲氨基-6-甲基尿嘧啶方便、高产率的合成方法. 以6-甲基尿嘧啶(1)为起始物, 经硝化、嘧啶N¹,N ³-烷基化、还原及氨基甲基化, 首次高产率合成了1,3-二(乙氧基甲基)-5- N,N -二甲氨基-6-甲基尿嘧啶(5), 并对其化学结构进行了表征.     

Azines and azoles: CXXV. New regioselective synthesis of 1-amino-6-methyluracils

Readily accessible 5-acetyl-4-hydroxy-3,6-dihydro-2H-1,3-thiazine-2,6-dione reacts with substituted hydrazines and carboxylic acid hydrazides under mild conditions to give the corresponding hydrazones. Under severe conditions (heating in boiling dimethylformamide) the reaction is accompanied by extrusion of COS with formation of substituted 1-amino-6-methyluracils. Reactions of 5-acetyl-4-hydroxy-3,6-dihydro-2H-1,3-thiazine-2,6-dione with monosubstituted alkyl-and arylhydrazines take different pathways, depending on the conditions. Heating of equimolar mixtures of the reactants in ethanol or propan-1-ol leads to the formation of 2-substituted 5-methyl-3-oxo-2,3-dihydro-1H-pyrazole-4-carboxamides rather than 1-amino-6-methyluracil derivatives.     

THE PHOTOREACTIONS AND FREE RADICAL INDUCED REACTIONS OF 1,3-DIMETHYLURACIL IN METHANOL AND OTHER ALCOHOLS

Abstract— Photoexcited 1,3-dimethyluracil (DMU) reacts with methanol to give 1,3-dimethyl-6-hydroxymethyl-5-hydrouracil ( 1 a) in addition to cyclobutane type dimers and 1,3-dimethyl-6-methoxy-5-hydrouracil ( 2 a). Free radical induced reaction, initiated by photodecomposition of di- t -butyl peroxide with light of wavelength greater than 290nm, leads to 1 a, 5,6-dihydroxymethyl-5,6-dihydro-1,3-dimethyl-uracil ( 1 d) and 6-hydroxymethyl-1,3-dimethyluracil as the products.     

Preparation and reaction of uracil substituted cyclen and cyclam: formation of tricyclic guanidinium and dihydroimidazolium salts

Di-uracil substituted cyclen derivatives were prepared by the reaction of cyclen with 6-chloro-1-methyluracil or 6-chloro-1,3-dimethyluracil. The reaction of cyclam with 6-chloro-1,3-dimethyluracil gave a similar di-uracil substituted cyclam. The 1,7-di-uracil substituted cyclen was converted to the tricyclic guanidinium salt and acylurea upon heating in DMSO in the presence of weak acid. The 1,8-di-uracil substituted cyclam gave a tricyclic dihydroimidazolium salt under the same conditions. These reactions can be explained by an intramolecular uracil ring-breaking reaction mechanism.     

Studies on the preparation and exchange reactions of 5-deuterated uracils

The mechanism of base catalyzed proton exchange at the 5-position of uracil and its N-methylated derivatives has been studied. These reactions proceed by addition — elimination across the 5,6-double bond when the 1-nitrogen is substituted with a methyl group, or with anchimeric assistance of the N-1 anion if the 1-position is unsubstituted. The base catalyzed hydrolyses of 1,3-dimethyluracil and 3-methyluracil also appear to proceed through hydrated intermediates. A facile method for an acid catalyzed preparation of 5-deuterated uracils is described as well as a simple and accurate method for analysis of deuterium content.     

Molecular and crystal structure of 5,6-diamino-1-methyluracil and 5,6-diamino-1,3-dimethyluracil monohydrate. Semiempirical calculations (AM1 and PM3) on 5,6-diaminouracil derivatives

The crystal and molecular structures of 5,6-diamino-1-methyluracil and 5,6-diamino-1,3-dimethyluracil monohydrate have been determined from X-ray diffraction. Both compounds are planar and the two amino groups have two different conformations. The substituent at the 5 position seems to be a true primary amino group with a strongly sp³ nitrogen, whereas the one at the 6 position is nearly coplanar with the uracil ring, displaying a predominant sp² character.Semiempirical calculations were made on 5,6-diaminouracil, 5,6-diamino-2-thiouracil and their endocyclic N-methylated derivatives using the AM1 and PM3 hamiltonians. These indicate that the stability decreases on increasing methylation, the 2-thio compounds always being less stable than the 2-oxo ones.     

Crystal structure of bromoalkyl derivatives of 6-methyl-uracil and isocyanuric acid

Single crystal XRD is used to study the crystal structure of 1-(4-bromobutyl)-3,6-dimethyluracil and 1,3-dimethyl-5-(5-bromopentyl)-isocyanurate in comparison with structurally similar compounds studied previously. It is shown that unlike macrocyclic compound, for which the crystal structure is determined by the presence of the stacking effect, in the crystals of their artificial precursors stacking interactions are not observed. For 1-(4-bromobutyl)-3,6-dimethyluracil, C-H...O interactions and C=O...Br interactions for 1,3-dimethyl-5-(5-bromopentyl)-isocyanurate are found. Original Russian Text Copyright ? 2009 by Yu. K. Voronina, L. F. Saifina, E. S. Romanova, O. A. Lodochnikova, and I. A. Litvinov __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 50, No. 3, pp. 608–611, May–June, 2009.     

Ferrocenyl-Pyrenes,Ferrocenyl-9,10-Phenanthrenediones,and Ferrocenyl-9,10-Dimethoxyphenanthrenes: Charge-Transfer Studies and SWCNT Functionalization

The synthesis of 1-Fc- ( 3 ), 1-Br-6-Fc- ( 5 a ), 2-Br-7-Fc- ( 7 a ), 1,6-Fc₂- ( 5 b ), 2,7-Fc₂-pyrene ( 7 b ), 3,6-Fc₂-9,10-phenanthrenedione ( 10 ), and 3,6-Fc₂-9,10-dimethoxyphenanthrene ( 12 ; Fc=Fe(η⁵-C₅H₄)(η⁵-C₅H₅)) is discussed. Of these compounds, 10 and 12 form 1D or 2D coordination polymers in the solid state. (Spectro)Electrochemical studies confirmed reversible Fc/Fc⁺ redox events between −130 and 160 mV. 1,6- and 2,7-Substitution in 5 a (E°′=−130 mV) and 7 a (E°′=50 mV) influences the redox potentials, whereas the ones of 5 b and 7 b (E°′=20 mV) are independent. Compounds 5 b , 7 b , 10 , and 12 show single Fc oxidation processes with redox splittings between 70 and 100 mV. UV/Vis/NIR spectroelectrochemistry confirmed a weak electron transfer between Fe^II/Fe^III in mixed-valent [ 5 b ]⁺ and [ 12 ]⁺. DFT calculations showed that 5 b non-covalently interacts with the single-walled carbon nanotube (SWCNT) sidewalls as proven by, for example, disentangling experiments. In addition, CV studies of the as-obtained dispersions confirmed exohedral attachment of 5 b at the SWCNTs.     

Experimental and quantum-chemical study of the mechanism of oxidation of 5-hydroxy-6-methyl-uracil by molecular oxygen in the presence of copper(II) ions

It has been discovered experimentally that 5,5,6-trihydroxy-6-methylpyrimidine-2,4-dione is formed on oxidizing 5-hydroxy-6-methyluracil with molecular oxygen in aqueous medium in the presence of copper(II) chloride. Ab initio and DFT calculations on the 6-31G* basis, both in the gas phase and allowing for solvent, showed that the process proceeds with the direct participation of an activated oxygen molecule on the complex CuCl₂·(5-hydroxy-6-methyluracil)2. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 586-593, April, 2009.