Synthesis of 1-(5,6-dihydro-2H-thiopyran-2-yl)uracil by a Pummerer-type thioglycosylation reaction: the regioselectivity of allylic substitution

1-(5,6-Dihydro-2H-thiopyran-2-yl)uracil derivatives, a new 4′-thio-D4-nucleoside analogue, were synthesized by reacting 5,6-dihydro-2H-thiopyran sulfoxide and persilylated uracil in a Pummerer-type thioglycosylation reaction. The reaction of 5-alkyl substituted dihydrothiopyran sulfoxide 7 only gave 1-(dihydrothiopyran-2-yl)uracil 9. On the other hand, the reaction with a 5-siloxy substituted derivative of 7 resulted in a mixture of products with the uracil moiety at either the α- or the γ-position. The use of a prolonged reaction time resulted in the exclusive formation of the 4-substituted dihydrothiopyran derivative 10. The result suggests that an equilibrium is operative in the formation of the α- and γ-adducts and that the latter should be more thermodynamically stable than the former. This conclusion was also supported by theoretical calculations.     

Oxidative cleavage of a cyclobutane pyrimidine dimer by photochemically generated nitrate radicals (no(3)*)

[reaction: see text] Photochemically generated nitrate radicals (NO(3)(*)) cleave the stereoisomeric N,N-dimethyl-substituted uracil cyclobutane dimers 1a-d into the monomeric uracil derivative 2 as the major reaction pathway. A preferred splitting of the syn dimers 1a,b was observed. The reaction is expected to proceed through initial one-electron oxidation with formation of an intermediate cyclobutane radical cation 11. In addition to cycloreversion, competing reaction steps of 11, which lead to the observed byproducts, are suggested.     

Synthetic studies towards the tunicamycins and analogues based on diazo chemistry. Total synthesis of tunicaminyl uracil

A synthetic approach to the tunicamycins, a complex family of nucleosides with potent antibiotic and antiviral activities is reported based on diazo chemistry. The corresponding precursors for the synthesis of tunicaminyl uracil derivatives, the non-stabilized diazo derived from 13 and the aldehyde derivative of uridine, compound 4, were prepared efficiently from commercially available D-galactal and uridine, respectively. After a high yielding coupling reaction to obtain the ketone 14, a stereoselective reduction provided the corresponding tunicaminyl uracil derivative 17a and its C-7 epimer 17b. The interconversion of the diazo and aldehyde functional groups in the requisite building blocks was similarly achieved to obtain the ketone 32, which after reduction yielded the corresponding 7-deoxy-6-hydroxy tunicaminyl uracil analogs 33a and 33b.     

Synthesis of 1-(2′-O-methyl-β-d-ribofuranosyl)-uracil (2′-O-methyluridine) and 3-(2′-O-methyl-β-d-ribofuranosyl)uracil

1-O-Acetyl-3,5-di-O-benzoyl-2-O-methyl-β-d-ribofuranose has been prepared in five steps from benzyl 2-O-methyl-β-d-ribopyranoside. Reaction of the furanose derivative with 2,4-bis-(trimethylsilyl)uracil in the presence of stannic chloride provides a new synthesis of 2′-O-methyl uridine and also yields the hitherto unknown 3-(2′-O-methyl-β-d-ribofuranosyl)uracil.     

Assisted intramolecular proton transfer in (uracil)2Ca2+ complexes

The structure and relative stability of the complexes between uracil dimers and Ca²⁺, as well as the proton transfer (PT) processes within these dimers, have been investigated by the density functional theory methods. Although in uracil dimers PT occurs as an almost synchronous double PT processes that connect the diketo dimer with a keto-enol dimer, the process within the most stable (uracil)₂Ca²⁺ complexes is much more complicated, and the product of the reaction looks like the result of an intramolecular PT from one of the NH groups of one monomer to one of the carbonyl groups of the same monomer. An analysis of the force profile along the reaction coordinate shows that the intimate mechanism implies three elementary steps, two intermolecular PTs, and an in-plane displacement of one monomer with respect to the other. The result of this so-called assisted intramolecular proton transfer is the formation of a dimer in which only one monomer is a keto-enol derivative, the other monomer being apparently unchanged, although it suffers significant structural rearrangements along the reaction coordinate. Quite importantly, this dimer is significantly stabilized upon Ca²⁺ association; therefore, while the most stable uracil dimers correspond systematically to associations involving only the diketo forms, in (uracil)₂Ca²⁺ complexes the most stable structures correspond to those in which one of the monomers is a keto-enol uracil isomer.     

Studies on 2'-alpha-C-carboxyalkyl nucleosides and their application to a stereocontrolled nucleobase exchange process

The ability of 2'-alpha-C-carboxyalkyl nucleosides to undergo an unusual two-step stereocontrolled nucleobase exchange process has been investigated. Upon silylation a protected 2'-deoxy-2'-alpha-C-(carboxymethyl)uridine derivative can undergo intramolecular displacement of the uracil base, by the 2'-carboxylic acid group, to form a pentofuranosyl gamma-lactone. Under identical conditions the homologous 2'-deoxy-2'-alpha-C-(carboxyethyl)uridine derivative does not yield the corresponding delta-lactone, but undergoes elimination of uracil to give the corresponding glycal. The pentofuranosyl gamma-lactone is a good substrate for nucleoside synthesis by the Vorbrüggen procedures and undergoes completely stereoselective ring opening with either pyrimidine or purine silylated nucleobases to give novel 2'-C-carboxymethyl beta-nucleosides in moderate to high yield.     

Acyclopyrimidine C-nucleosides: Synthesis of 5-[(2,3-dihydroxy-1-propoxy)methyl]pyrimidines

From the condensation of 5-hydroxymethyluracil and glycerine, 5-[(2,3-dihydroxy-1-propoxy)methyl]uracil ( 3 ) was synthesized, which was converted to the isocytosine derivative 9 by the ring-transformation reaction via dimethyluracil derivative 7 .     

Can cytosine, thymine and uracil be formed in interstellar regions? A theoretical study

This theoretical study investigates possible synthetic routes to cytosine, uracil and thymine in the gas phase from precursor molecules that have been detected in interstellar media. Studies at the CCSD(T)/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory suggest that: The reactions between :CCCNH and :CCCO with monosolvated urea may constitute viable interstellar syntheses of cytosine and uracil. No low energy equilibration between cytosine and uracil has been demonstrated. The interaction of :CH(2) with the 5 C-H bond of uracil may form thymine in an energetically favourable reaction, but competing reactions where :CH(2) reacts with double bonds and other CH and NH bonds of uracil, reduce the effectiveness of this synthesis. The reaction between the hydrated propional enolate anion and isocyanic acid may produce thymine, in a reaction sequence where ΔG(reaction)(298 K) is -22 kJ mol(-1) and the maximum energy requirement (barrier to the first transition state) is only 47 kJ mol(-1).     

Identification of ionic and tautomeric species of uracil by second derivative UV absorption spectroscopy.

The individual UV absorption spectra of ionic and tautomeric species of uracil and eight derivatives have been determined by second derivative spectroscopy. Second derivative bands have been ascribed to different species by taking into account the proportion of each molecular species at each pH value and the tautomer fixed for derivatives. Theoretical results in the literature are in good agreement with the observed λ_Min(D^2nd) positions of both N(1)- and N(3)- uracil monoanion and dianion. Neutral uracil species (diketo form) presents six second derivative bands (two in normal spectra). For the three higher electronic transition energies, the discrepancy between calculated and experimental values does not exceed 0.05 e V. Literature assignment from normal spectra for the N(3)- anion are ππ* transitions but our results show that n π* are possible too.     

N-Aminoderivate des Uracils (1. Mitt.)

Zusammenfassung Das N-1-Aminouracil¹ (II) wird auf 2 verschiedenen Wegen erhalten. Es werden einige Aldehydderivate und das Benzophenonderivat dieses cyclischen Semicarbazids dargestellt. Das Na-Salz des Benzylidenderivates von II ist selektiv am N-3 alkylierbar. Das 1-Amino-3-(n-butyl)-uracil (XII) wird mit Toluolsulfochlorid oder mit p-Toluolsulfonylisocyanat acyliert. Das 1-Aminouracil (II) und das 1-Amino-3-methyluracil (XI) gaben mit HNO₂ Uracil bzw. 3-Methyluracil und N₂O. Die Bildung des 3-Methyluracils dient als Strukturbeweis für II. Das 1,3-Diaminouracil tritt beim Umsatz von Uracil mit Hydroxylamin-O-sulfonsäure als Zweitprodukt neben 1-Aminouracil auf.

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N-1-Aminouracil (II) has been obtained in two different ways. Several aldehydes and the benzophenone derivative have been prepared from this cyclic semicarbazide. The sodium salt of the benzylidene derivative of II undergoes selective alkylation at N-3. 1-Amino-3-(n-butyl)-uracil can be acylated with toluenesulfonyl chloride or p-toluenesulfonyl isocyanate. Reaction of II or 1-amino-3-methyl-uracil (XI) with nitrous acid yielded uracil and 3-methyl-uracil, respectively, and N₂O. Formation of 3-methyl-uracil confirms the structure of II. 1,3-Diaminouracil has been found to be a byproduct of the reaction between uracil and hydroxylamine-O-sulfonic acid besides II.

     

Carbocyclic analogs of cytosine nucleosides

The carbocyclic analogs of cytidine, 2′-deoxycytidine, and 3′-deoxycytidine were synthesized from the analogous uracil derivatives. The route consists of complete benzoylation of the uracil derivative, selective removal of a benzoyl group attached to the pyrimidine ring, conversion of the 4-oxo to a 4-chloro group with the dimethylformamide-thionyl chloride reagent, and replacement of the chloro group with an amino group in methanolic ammonia. When the total products of the deoxychlorination reaction were employed, the desired cytosine derivatives were frequently accompanied by small amounts of the corresponding N,N-dimethylcytosine derivatives, which could be removed by ion-exchange chromatography. Carbodine (VIa), the carbocyclic analog of cytidine, was obtained in 84% yield from the pure 4-chloropyrimidinone intermediate, after the latter was prepared by deoxychlorination in carbon tetrachloride. Carbodine has antileukemic, antiviral, and antibacterial activity.     

Synthetic approach toward antibiotic tunicamycins — VI total synthesis of tunicamycins

Tunicamycins and their eight analogs have been synthesized by condensation of a N-acetyl-D-glucosamine derivative and an anomeric chloride of tunicaminyl uracil, followed by deprotections and N-acylation.     

A novel and specific fluorescence reaction for uracil

Facile and specific methods to quantify a nucleobase in biological samples are of great importance for diagnosing disorders in nucleic acid metabolism. In the present study, a novel fluorogenic reaction specific for uracil has been developed. The reaction was carried out in an alkaline medium containing benzamidoxime and K₃[Fe(CN)₆] which were heated for 2.0 min. Under the optimum reaction conditions, strong fluorescence was produced only from uracil, not from other many biogenic compounds tested such as cytosine, thymine, adenine, guanine, nucleobases, nucleosides, nucleotides, amino acids, saccharides, creatine, creatinine and urea. The sensitivity of this method was compared with a known fluorogenic reaction using phenacylbromide which does not react with uracil but reacts with cytosine, adenine and their analogues. The proposed uracil-specific reaction showed approximately 400-fold higher sensitivity than the phenacylbromide reaction. The lower detection limit of uracil by the present method was 100 pmol mL⁻¹, and a good linearity of the calibration curve was obtained up to 100 nmol mL⁻¹ uracil. Due to its high sensitivity and specificity, the quantitative determination of uracil was possible by the proposed fluorimetric method.     

A versatile route to potential dihydrofolate reductase inhibitors via the hitherto unknown 6-benzyl-2-(O-methyl)uracils: Synthesis of isotrimethoprim

The synthesis of 2, 4-diamino-6-(3, 4, 5-trimethoxybenzyl)pyrimidine (isotrimethoprim) has been accomplished starting from 2-(O-methyl)-6-(3, 4, 5-trimethoxybenzyl)uracil by standard procedures. The benzyluracil derivative has been obtained by reacting O-methylisourea sulphate and ethyl 3, 4, 5-trimethoxyphenacetylace-tate.     

Specific recognition of a nucleobase-functionalized poly(3,4-ethylenedioxithiophene) (PEDOT) in aqueous media

In this Letter we report the synthesis, characterization, and electrochemical investigation of a 3,4-ethylenedioxythiophene (EDOT) derivative covalently linked to the nucleobase uracil. The successful electrochemical polymerization of this derivative has provided modified electrodes with a novel functional poly(3,4-ethylenedioxythiophene) derivative. Recognition experiments in aqueous media have shown the specific recognition of the complementary base adenine. The electrochemical detection of the selective binding of nucleobases to this PEDOT derivative in aqueous media can be of particular interest for electrochemical sensor applications in physiological media.     

New routes to 1-deoxy-(3,4-dihydro-7,8-dimethyl-2,4-dioxopyrimido[4,5-b]-quinolin-10(2H)yl)-D-ribitols (5-deazariboflavins)

The acid-catalyzed reaction of 6-(N-D-ribityl-3,4-xylidino)uracil ( 1 ) with trimethyl ortho-formate yields a bis(methoxymethylene) derivative ( 2 ), which is readily deprotected to give 5-deazariboflavin ( 3 ). Correspondingly, 5-methyl-5-deazariboflavin ( 6 ) is produced by cyclization of the tetraacetate of 1 with acetyl chloride in the presence of stannic chloride followed by deacetylation.     

Synthesis and Characterization of Multithiouracils

Alkylation of bases group of nucleic acid, thymine and uracil, has attracted great attention. In order to investigate the intermolecular interactions, [1,2] and the photoreactions[3,4] between bases group of nucleic acid, many studies were focused on the synthesis of bisbases in the formation of B-(CH2)n-B (B′) in which trimethylene was commonly used as linker. Thiouracil is an important derivative of nucleic acid bases, and it can interfere with the synthesis of thyroxine, especially in the treatment of hyperthyroidism and angina. However, to our knowledge, the synthesis of bisthiouracils, even trithiouracils, using flexible or rigid linkers has not been reported. Herein, we have synthesized eight thiouracil derivatives by nucleophilic reaction between thiouracil and varied bromides. All the compounds have been characterized by IR, 1H NMR and element analysis.     

Comparative absorption spectroscopy involving 4f-4f transitions to explore the kinetics of simultaneous coordination of uracil with Nd(III) and Zn(II) and its associated thermodynamics

The interaction of uracil with Nd(III) has been explored in presence and absence of Zn(II) using the comparative absorption spectroscopy involving the 4f-4f transitions in different solvents. The complexation of uracil with Nd(III) is indicated by the change in intensity of 4f-4f bands expressing in terms of significant change in oscillator strength and Judd-Ofelt parameters. Intensification of this bands became more prominent in presence of Zn(II) suggesting the stimulative effect of Zn(II) towards the complexation of Nd(III) with uracil. Other spectral parameters namely Slator-Condon (F(k)'s), nephelauxetic effect (β), bonding (b(1/2)) and percent covalency (δ) parameters are computed to correlate their simultaneous binding of metal ions with uracil. The sensitivities of the observed 4f-4f transitions towards the minor coordination changes around Nd(III) has been used to monitor the simultaneous coordination of uracil with Nd(III) and Zn(II). The variation of intensities (oscillator strengths and Judd-Ofelt parameters) of 4f-4f bands during the complexation has helped in following the heterobimetallic complexation of uracil. Rate of complexation with respect to hypersensitive transition was evaluated. Energy of activation and thermodynamic parameters for the complexation reaction were also determined.     

A highly stereoselective samarium diiodide-promoted aldol reaction with 1'-phenylseleno-2'-keto nucleosides. Synthesis of 1'alpha-branched uridine derivatives

Since 1'-branched nucleosides are biologically important targets in medicinal chemistry, more efficient methods for preparing them are required. The 1'alpha-branched uridine derivatives were successfully synthesized via a samarium diiodide (SmI(2))-promoted aldol reaction. Treatment of the 1'alpha-phenylseleno-2'-ketouridine derivative 6, readily prepared from uridine, with SmI(2) at -78 degrees C in THF reductively cleaved the anomeric Se-C bond to generate the corresponding samarium enolate, which was highly stereoselectively condensed with aldehydes, such as PhCHO, MeCHO, i-PrCHO, or (CH(2)O)(n)(), to give the corresponding 1'alpha-1' 'S-branched products 12a-d. This is the first time an enolate has been generated by reductively cleaving a C-Se bond. The highly selective stereochemical results suggest that the aldol reaction proceeds via a chelation-controlled transition state. When an excess of aldehyde was used and the reaction mixture was gradually warmed, the tandem aldol-Tishchenko reaction proceeded to give the "arabino-type" nucleosides 14a-c, having a 2'-"up" hydroxyl and 1'alpha-1' 'S-branched chain. 1'alpha-Hydroxymethyluridine (21), which is the uracil version of the antitumor antibiotic angustmycin C, was synthesized from the aldol reaction product 10.     

Specific Intermolecular Interactions in the Supramolecular Structure of 5‐Hydroxy‐6‐Methyluracil: A DFT Study of the Hydrogen‐bonded Dimers

Studying the self‐assembly of uracil derivatives has great importance for biochemistry and nanotechnology. For example, modification of the sorbent surfaces by 5‐hydroxy‐6‐methyluracil (HMU ) enhances their adsorption activity. It is assumed that these changes are caused by the self‐assembly of the network‐like supramolecular associates of the uracil derivative on the sorbent surface. In the present work, the relative stabilities of 15 hydrogen‐bonded dimers HMU have been studied by the TPSSh /TZVP density functional theory method and the strengths of the noncovalent interactions analyzed in terms of the reduced density gradient and natural bond orbital approaches. It was found that the symmetric dimer stabilized by two intermolecular hydrogen bonds N1 –H∙∙∙O–C2 (dimer 1‐1) is the most stable. This suggests that the self‐assembly of HMU should occur through the intermediate formation of the dimer 1‐1. The results may be useful for understanding the processes of self‐assembly of the uracil derivatives and the rationalized design of the uracil‐based supramolecular structures with specific properties.