Carbon-13 NMR spectra of nucleoside 3′,5′-cyclic phosphates. Proposition for revised signal assignments

On the basis of the data obtained from ¹³C NMR spectra of 8,2′-S-cycloadenosine 3′,5′-cyclic phosphate and other nucleoside 3′,5′-cyclic phosphate analogues, it is suggested that the published assignments of the C-3′ and C-4′ signals in nucleoside 3′,5′-cyclic phosphates should be reversed. According to the revised assignments, C-4′, which is fixed very closely to the diesterified phosphate group is markedly shielded (?12.5 to ?15 ppm), and the C-3′ signal shows a downfield shift (+6 to +8 ppm) which is comparable to that for the C-5′ signal, for all compounds so far measured when compared with the chemical shifts for the corresponding nucleosides. The 3′,5′-cyclic phosphates of thymidine and 8,2′-S-cycloadenosine, which have no α-OH group on C-2′, show similar chemical shift changes for the corresponding sugar carbons which are different from those observed for ribonucleoside derivatives.     

Syntheses of 6,8-disubstituted-9-β-D-ribofuranosylpurine 3′,5′-cyclic phosphates

A series of 6,8-disubstituted-9-β-D-ribofuranosylpurine 3′,5′-cyclic phosphates were prepared employing preformed 9-β-D-ribofuranosylpurine 3′,5′-cyclic phosphate precursors. Three synthetic approaches were utilized to accomplish the syntheses. The first approach involved a study of the order of nucleophilic substitution, 6 vs 8, of the intermediate 6,8-dichloro-9-β-D-ribofuranosyipurine 3′,5′-cyclic phosphates ( 2 ) with various nucleophilic agents to yield 8-amino-6-chloro-, 8-chloro-6-(diethylamino)-, 6-chloro-8-(diethylamino)-, 6,8-bis-(diethylamino)- and 8-(benzylthio)-6-chloro-9-β-D-ribofuranosylpurine 3′,5′-cyclic phosphate (4, 9, 10, 11, 13) respectively and 6-chloro-9-β-D-ribofuranosylpurin-8-one 3′,5′-cyclic phosphate ( 5 ) and 8-amino-9-β-D-ribofuranosylpurine-6-thione 3′,5′-cyclic phosphate ( 6 ). The order of substitution was compared to similar substitutions on 6,8-dichloropurines and 6,8-dichloropurine nucleosides. The second scheme utilized nucleophilic substitution of 6-chloro-8-substituted-9-β-D-ribofuranosylpurine 3′,5′-cyclic, phosphates obtained from the corresponding 8-subslituted inosine 3′,5′-cyclic phosphates by phosphoryl chloride, 6,8-bis-(benzylthio)-, 6-(diethylamino)-8-(benzylthio),8-(p-chlorophenylthio(-6-(diethylamino)- and 6,8-bis-(methyl-thio)-9-β-D-ribofuranosylpurine 3′,5′-cyclic phosphates ( 14, 12, 20 , and 21 ) respectively, were prepared in this manner. The final scheme involved N¹-alkylation of an 8-substituted adenosine 3′,5′-cyclic phosphate followed by a Dimroth rearrangement to give 6-(benzylamino)-8-(methylthio)- and 6-(benzylamino)-8-bromo-9-β-D-ribofuranosylpurine 3′,5′-cyclic phosphate ( 24 and 25 ).     

The Effect of Trifluoroethoxy Groups on the Structures of Eight-Membered Ring-Containing Cyclic Phosphites 1

New phosphites 1–4 were synthesized from phosphorus trichloride and an appropriate diphenol followed by the addition of trifluoroethanol in the presence of triethylamine. These phosphites are to serve as precursors in the syntheses of biorelated hypervalent phosphoranes. ¹H, ¹⁹F, and ³¹P NMR spectra were recorded. X-ray analysis of 3 and 4 revealed that the sulfur-containing eight-membered ring was in a syn conformation that a allowed a sulfur donor interaction to the phosphorus atom, whereas for phosphite 2, the eight membered sulfonyl containing ring was in an anti conformation that did not allow a donor interaction to phosphorus from the oxygen atom of the sulfonyl group. Structural comparisons are made with related cyclic phosphites and phosphates having donor atoms in eight-membered rings.     

Phosphate-Phosphonate Rearrangement of Aliphatic Phosphates

Abstract

Phosphorylation of various aliphatic alcohols gives phosphates 1 which are deprotonated by sBuLi/TMEDA in diethyl ether, THF or hexane at ?78 °C. The organo-lithiurns 2 and 4 formed isornerize to α-hydroxy- phosphonates 3 and 5 (phosphate-phosphonate rearrangement^[1.2]     

Enzymatic Synthesis of Inositol Phosphodiesters Using Phosphatidylinositol-Specific Phospholipase C

Abstract

Transesterication of inositol 1,2-cyclic phosphate with primary alcohols in the presence of phospholipase C produces alkyl inositol phosphates.     

Products in the Reactions of Trialkyl Phosphites with α-Halogeno-acetophenones in Alcoholic Media

Abstract

α-Hydroxyphosphonates are formed, in addition to vinyl phosphates and dehalogenated ketones, in the reactions of trimethyl phosphite (in methanol) or triethyl phosphite (in ethanol) with variously substituted α-chloro, α-bromo, and α,α,-dichloro-acetophenones. Tri-isopropyl phosphite in propan-2-ol gives only the vinyl phosphate. Ketophosphonates are not detectable amongst the reaction products under the conditions used. Trends in product composition can be correlated with the leaving ability of halogen, substituent effects, structure of the phosphite, and reaction temperature. Reactant ratios may also influence the product composition. The reactions of trimethyl phosphite in methanol with 4-nitro-α-chloroacetophenone, or α,α-dichloroacetophenones yield the dehalogenated α-hydrogxyphosphonates in addition. In the case of the 4-nitro derivative, this product cannot be accounted for by reaction of the phosphite with dehalogenated ketone (4-nitroacetophenone). Dehalogenation of the first-formed α-hydroxyphosphonate was, however, shown to occur under reaction conditions and appears to require the removal of positive chlorine, followed by protonation. Reactions of the α,α-dichloroacetophenones were similar to those of the α-chloroacetophenones, giving the corresponding chlorovinyl phosphate, α,α-dichloro-α-hydroxyphosphonate, and monodehalogenated ketone(i.e. α-chloroacetophenone); the latter was not however detected as it reacted further with excess phosphite to give the expected products as described above. Possible mechanisms for the various reactions are discussed. The ¹H and ¹³C nmr spectra of the α-hydroxy-phosphonates show magnetic non-equivalence of the two alkoxy groups, attributed to restricted rotation about the P-C bond as a result of intramolecular hydrogen-bonding.     

Inositol Monophosphates Prepared in a Single Step from Myo-Inositol and Inorganic Phosphate

ABSTRACT

A mixture of myo-inositol and inorganic metaphosphate (prepared by freeze drying an aqueous solution at pH 4) produced, upon warming, in moderate yield every inositol monophosphate ester, thereby providing in a single step a complete library of these compounds. The individual inositol monophosphates, both meso-compounds and racemic mixtures of the two pairs of enantiomers, were isolated by ion-exchange chromatography which was facilitated by the addition of borate to the mobile phase. The phosphates were characterised using phosphorus analysis in conjunction with alkaline phosphatase, mass spectrometry and ¹H NMR spectroscopy.     

Phosphorylation of Amine Compounds with Sodium Cyclo-triphosphate

Abstract

Among inorganic linear and cyclic phosphates, cyclo-triphosphate has drawn special attention for its high reactivity with various amine compounds. A ring opening reaction to produce N-alkylamidotriphosphate derivatives proceeds under moderate conditions, e.g., at room temperature in aqueous solution. In spite of its potentiality as a phosphorylating agent for amino groups, a systematic investigation on the reaction mechanism has not fully carried out. This may be due to the lack of analytical methods which allow the quantitative examination of the reactions. In this work, HPLC with an anion-exchanger column developed for phosphate compounds together with ³¹P-NMR were applied to a kinetic study. It has been clarified that; 1) the reactivity of amine compounds is primarily correlated with the basisity of the amino groups, i.e., pKa values of its conjugate acids, though, branching at α carbon of the amino group greatry retards the reaction rate because of steric hindrance, and 2) some bifunctional reagents, such as ethylenediamine, propanediamine, ethanol-amine, and some α-amino acids produce heterocycles which contain P-N bond through an intramolecular reaction following the ring opening of cyclo-triphosphate. Ba or Mg salts of N-alkylamidotriphosphate derivatives have been prepared from mono amines, diamines, aminoalcohols, and aminoacids.     

Synthesis of 2-(2-Thienyl)benzimidazoles by the Reaction of 2-(Mercaptomethyl)benzimidazole With β-Electrophilic Esters

New 2-(2-di- and tetrahydrothienyl)benzimidazole compounds were prepared by the ring closure reactions of 2-(mercaptomethyl)benzimidazole^1,2 (1) and α,β-unsaturated compounds activated with electron-withdrawing groups.     

Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway

In Escherichia coli , internalization and catabolism of organophosphonicacids are governed by the 14-cistron phnCDEFGHIJKLMNOP operon. The phnP gene product was previously shown to encode a phosphodiesterase with unusual specificity toward ribonucleoside 2',3'-cyclic phosphates. Furthermore, phnP displays shared synteny with phnN across bacterial phn operons. Here the role of PhnP was examined by (31)P NMR spectrometry on the culture supernatants of E. coli phn mutants grown in the presence of alkylphosphonic acid or phosphite. The addition of any of these alkylphosphonic acids or phosphite resulted in the accumulation of α-D-ribosyl 1,2-cyclic phosphate and α-D-ribosyl 1-alkylphosphonate in a phnP mutant strain. Additionally, α-D-ribosyl 1-ethylphosphonate was observed to accumulate in a phnJ mutant strain when it was fed ethylphosphonic acid. Purified PhnP was shown to regiospecifically convert α-D-ribosyl 1,2-cyclic phosphate to α-D-ribosyl 1-phosphate. Radiolabeling studies revealed that 5-phospho-α-D-ribosyl 1,2-cyclic phosphate also accumulates in a phnP mutant. This compound was synthesized and shown to be regiospecifically converted by PhnP to α-D-ribosyl 1,5-bisphosphate. It is also shown that organophosphonate catabolism is dependent on the synthesis of 5-phospho-α-D-ribosyl 1-diphosphate, suggesting that this phosphoribosyl donor is used to initiate the carbon-phosphorus (CP) lyase pathway. The results show that 5-phospho-α-D-ribosyl 1,2-cyclic phosphate is an intermediate of organophosphonic acid catabolism, and it is proposed that this compound derives from C-P bond cleavage of 5-phospho-α-D-ribosyl 1-alkylphosphonates by CP lyase.     

Conversion of Cyclic Phosphorothioates into Halophosphates and Neutral Phosphorus Esters and Amides

Abstract

Cyclic phosphorus esters and amides in the 1,3,2-dioxaphosphorinane-2-one series are usually obtained by the condensation of a diol with a suitable phosphorus oxyhalide. In the case of dissymetric diols the formation of two diastereoisomeric products, epimeric at phosphorus, can be expected. This procedure failed or proceeded with low yields when applied to the preparation of cyclic phosphates which would lead to the formation of sterically strained dioxaphosphorinane ring.¹     

The relationship between proton–proton NMR coupling constants and substituent electronegativities. II—conformational analysis of the sugar ring in nucleosides and nucleotides in solution using a generalized Karplus equation

The relationship between vicinal NMR proton–proton coupling constants and the pseudorotational properties of the sugar ring in nucleosides and nucleotides is reinvestigated. Compared with our earlier study several important improvements are introduced: first, a new empirical generalization of the classical Karplus equation is utilized, which allows an accurate correction for the effects of electronegativity and orientation of substituents on ³J(HH); second, empirical correlations between the parameters governing the conformation of β-D -furanosides (taken from an analysis of 178 crystal structures) were used to define proton–proton torsion angles as a function of the pseudorotation parameters P and Φ_m; and, third an iterative least-squares computer program was devised to obtain the best fit of the conformational parameters to the experimental coupling constants. NMR data for the sugar ring in the following compounds were taken from the literature and analysed: 3′,5′-cyclic nucleotides, a base-stacked ribonucleotide, 2′-anhydroarabinonucleosides, α-D -2′,2-O-cyclouridine, 2′- and 3′-aminosubstituted ribonucleosides, 2′- and 3′-deoxyribonucleosides. The present results confirm that the conformational properties found in the solid state are, on the whole, preserved in solution.     

The Synthesis of Substituted α, β-Butenolides from γ-Hydroxy-α, β-Acetylenic Esters

Abstract

The α, β-butenolide ring system is found in a number of physiologically important natural products² and there has been recent interest in the development of methods of synthesis of compounds of this type.³ It is well known that α, β-unsubstituted butenolides may be prepared by catalytic hydrogenation of γ-hydroxy acetylenic acids.^4,5b Recently, an excellent route of γ-hydroxy acetylenic esters which involves the addition of the lithium acetylide salts of propiolic esters to aldehydes⁵ and ketones⁶ has become available. We have carried out the addition of ethyl lithiopropiolate (1) to cyclohexanone (2) and 4-t-butylcyclohexanone (3) and wish to report the conversion of these adducts into corresponding β-methyl or β-methyl-α-allyl-α, β-butenolides.     

CONFORMATION OF EIGHT-MEMBERED DIOXATHIASILOCIN HETEROCYCLES IN SOLUTION

Abstract

The dibenzo[d,g][1,3,6,2]dioxathiasilocin derivatives 3a-f were prepared by the reaction of the thiobisphenols 1a-b with the corresponding dichlorosilanes 2a-e using triethylamine as an acid acceptor. The free energy of activation for ring inversion of the 2,4,8,10-tetra-tert-butyl-substituted 3a was determined by variable temperature ¹H NMR to be 13.9 kcal/mol. The ¹H NMR spectral data of 3a requires that the ring conformer possess a σ plane of symmetry passing through the silicon and bridging sulfur atoms. In the variable temperature ¹H NMR spectra of the 2,4,8,10-tetramethyl-substituted 3b no evidence was observed for the slowing of ring inversion at-55^oC, suggesting that the energy of activation for ring inversion is less than 10.9 kcal/mol. The ¹H NMR spectral data of 3e-f indicates the presence of equilibrating conformational isomers. The results of this study supports the suggestion that steric factors are a major contributor to the barrier of ring inversion for the dibenzo-[d, g][1,3,6,2]dioxathiasilocin ring system.     

NEW EVIDENCE FOR ISOMERISM OF THE FORMAZYL GROUP. SYNTHESIS OF SELECTIVELY PROTECTED 2-DEOXY-GALACTOSE FORMAZANS

A new application of the formazyl activation provided selectively protected new derivatives of both 2-deoxy-D-galactose and 2-acetamido-2-deoxy-D-galactose formazans from 6-amino-6-deoxy-D-galactose 6,4-cyclic carbamate (1) under very simple conditions. The ¹H NMR spectrum of the acetylated 2-deoxy derivative 7 revealed an equilibrium between chelated and unusual non-chelated forms of the formazan moiety in solution.     

The Effect of Silver Perchlorate of the Reaction of Trialkyl Phosphite with α-Halogenoketones

Abstract

Trialkyl phosphites are known to react with α-halogenoketones to yield β-ketophosphonates (Arbuzov product) or vinyl phosphates (Perkow product) according to coniiitions.¹ α-Hydroxyphosphonate may be formed in addition, in prcltic media.² We have now shown that none of these products is formed in the presence of silver perchlorate (in benzene sclutim); nor could we detect the ketophosphonium perchlorate reported previously. Phosphorus-31 nmr showed the formation of trimethyl phosphate and tetramethyl pyrophosphate as the exclusive phosphorus-containing products. The sequence of possible reaction is complex and the overall stoichiometry may vary somewhat according to the rate and order of rixing. Trialkyl phosphate could be formed by elimination of alkyne from vinyloxyphosphonium intermediate produced together with silver iodine in first stage of the interaction. Pyrophosphate formation would then result from nucleophilic attack of trimethyl phosphate on the trimethoxy(1-nethylvinyloxy)phosphoniun ion, which may be formed as a reactive intermediate. Evidence for formation of methyl perchlorate in the final dealkylation of the quasiphosphonium intermediate is provided by proton nmr spectroscopy and by the formation of the N-methylquino-linium salt on addition of quinoline. No change in the ³¹P nmr spectrum occurs at this stage. Other by-products of the main reactions include the dehalogenated ketone (acetone from iodoacetone or acetnphenone from α-iodoacetophenone).     

1H NMR Study of Methyl O-Acetyl-α-and-β-D-Xylopyranosides Conformational Studies and Non Additivity of 1H-Shift Increments

Abstract

¹H NMR spectra of the complete series of fully and partially acetylated methyl α-and β-D-xylopyranosides have been studied. The α-anomers occur exclusively in ⁴C₁ chairs but the ¹C₄ chair becomes increasingly populated in the β-forms especially when the OH-3 is not acetylated. Increments used for the prediction of the chemical shifts of ring protons are discussed and compared with the literature data. The predictability for changes in shifts upon acetylation is poor.     

The NMR Coupling Constants,and Conformational and Structural Properties of Flexible Aldopyranosyl Rings: α- and β-D-Idopyranose

ABSTRACT

The flexible ring structures of α- and β-D-idopyranose have been investigated by conformational analysis using structures generated by MacroModel and GMMX search protocols. The lowest energy structures found during the conformer search for the ⁴ C ₁, ¹ C ₄, ^O S ₂ and the ³ S ₁ structures were then examined by AM1 and Gaussian ab initio methods at the HF/6-311G** and HF/6-31+G* levels. The B _2,5 conformer found for β-D-idopyranose at 14 kJ/mol by GMMX and 29.5 kJ/mol for α-D-idopyranose by MacroModel would not contribute to Boltzmann-averaged ¹H NMR coupling constants. The Merck MMFF force field tends to overweight the ¹ C ₄ structures, making these the lowest energy conformers for both anomers. Boltzmann-averaged coupling constants are heavily weighted by this structure in the MMFF search conformer ensemble. Averaged proton coupling constants determined using MMFF fit very well for α-D-idopyranose compared to the observed values, but fit poorly for the β-anomer. Ab initio results place the ¹ C ₄ conformer at lowest energy for the α-anomer and place the ⁴ C ₁ conformer at lowest energy for the β-anomer. The GMMX and MM3* force fields find the ⁴ C ₁ conformer to have the lowest energies for both anomers.     

Design,Synthesis, and Antiviral Activity of α-Aminophosphonates Bearing a Benzothiophene Moiety

Abstract

A series of α-aminophosphonates containing a benzothiophene moiety was designed and synthesized. All synthesized compounds were confirmed by ¹H NMR, ¹³C NMR, ³¹P NMR, infrared spectroscopy, and elemental analysis. The half-leaf method was used to determine the in vivo efficacy of α-aminophosphonates bearing a benzothiophene moiety against the tobacco mosaic virus (TMV). Bioassay results showed that all compounds exhibited certain anti-TMV activity at 500 μg/mL concentration. Compound 2f exhibited a curative effect of up to 48.1% against TMV, which was almost similar to that obtained from the standard ningnanmycin (51.9%).

[Supplementary materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfer, and Silicon and the Related Elements for the following free supplemental files: Additional text, figures, and tables.]     

Deuterated Disaccharides for the Investigation of Protein-Carbohydrate Interactions-Application of Bioaffinity-and STD-NMR

ABSTRACT

NMR spectroscopic analysis of carbohydrates often suffers from severe overlap of resonance signals, especially in ¹H NMR spectra. Therefore, we synthesized four 2,3,4-trideuterio-α-L-fucose containing disaccharides, α-L-Fuc-(1→6)-β-D-GlcNAc-OMe 1, α-L-Fuc-(1→4)-β-D-GlcNAc-OMe 2, α-L-Fuc-(1→3)-β-D-GlcNAc-OMe 3, and α-L-Fuc-(1→2)-β-D-Gal-OMe 4. Compounds 1 to 4 are well suited to be subjected to NMR conformational analysis because their ¹H NMR spectra show almost no overlap of signals. The deuterated disaccharides 1 to 4 will therefore be used as NMR probes for the exploration of fucose-binding proteins. With a mixture of the corresponding non-deuterated disaccharides it is demonstrated that recently developed parallel NMR screening protocols, Bio-Affinity NMR and STD-NMR, deliver fast and robust tools to assay the compounds synthesized for protein-binding affinity.