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.     

Investigation of the torsional angle at the glycosidic bond in 5′-amino-5′-deoxythymidine derivatives by carbon-13 n.m.r. spectroscopy

The conformational preference of the thymine base ring with respect to the sugar ring in β,β,β,-trichloroethyl 5′amino-5′-deoxythymidine-5′-phosphate has been studied by ¹³C n.m.r. spectroscopy. The magnitude of the three bond vicinal coupling constant, J(C-2, H-1′), for β,β,β-trichloroethyl 5′-amino-5′-deoxythymidine-5′-phosphate and the similarity between the chemical shifts for the furanose carbons C-1′, C-2′, and C-3′ in β,β,β-trichloroethyl 5-′-amino-5′-deoxythymidine-5′-phosphate and in β,β,β-trichloroethyl thymidine 5′-phosphate indicate that the amino analogue exists in aqueous solution predominantly in the anti conformation, as is the case with natural nucleotides.     

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.     

On the assignments of carbon-13 NMR spectra of cyclic nucleotides

Two conflicting assignments have been proposed for the ¹³C NMR signals of 3′,5′-cyclic nucleotides. This communication describes selective decoupling experiments for several cyclic nucleotides which provide the correct assignment based on unambiguous experimental evidence.     

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 ).     

Preparation of diastereomeric thymidine 3′,5′-cyclic methylphosphonates. Assignment of RP and SP configurations by 13C NMR

The diastereomers of thymidine 3′,5′-cyclic methylphosphonate have been prepared and separated. A use of ¹³C NMR for the assignment of their phosphorus configurations is demonstrated which should be generally applicable to P-derivatized cyclic nucleotides.     

High Accuracy of Karplus Equations for Relating Three‐Bond J Couplings to Protein Backbone Torsion Angles

³J_C′C′ and ³J_HNHα couplings are related to the intervening backbone torsion angle ${\varphi }$ by standard Karplus equations. Although these couplings are known to be affected by parameters other than ${\varphi }$ , including H‐bonding, valence angles and residue type, experimental results and quantum calculations indicate that the impact of these latter parameters is typically very small. The solution NMR structure of protein GB3, newly refined by using extensive sets of residual dipolar couplings, yields 50–60 % better Karplus equation agreement between ${\varphi }$ angles and experimental ³J_C′C′ and ³J_HNHα values than does the high‐resolution X‐ray structure. In intrinsically disordered proteins, ³J_C′C′ and ³J_HNHα couplings can be measured at even higher accuracy, and the impact of factors other than the intervening torsion angle on ³J will be smaller than in folded proteins, making these couplings exceptionally valuable reporters on the ensemble of ${\varphi }$ angles sampled by each residue.     

13C nuclear magnetic resonance spectroscopy of selected adenine nucleosides: Structural correlation and conformation about the glycosidic bond

Structural correlations have been carried out from ¹³C chemical shifts (δ) and by analysis of ¹J(CH) coupling constants, and the conformation about the glycosidic bond has been studied by means of the ³J(CH) vicinal coupling constants between C-8 and H-1′ of some adenine nucleosides such as adenosine (Ado), N(7)-β-D-ribofuranosyladenine (N(7)-Ado), N(9)- and N(7)-β-D-xylofuranosyladenine (N(9)-xylAde and N(7)-xylAde), N(9)-(3-chloro-3-deoxy-β-D-xylofuranosyl)adenine (3′-Cl-xylAde) and N(9)-(2-chloro-2-deoxy-β-D-arabinofuranosyl)adenine (2′-Cl-araAde). The analysis of the influence on δ¹³C of the nature and configuration of the substituent in the carbohydrate fragment of the molecule has revealed two types of effects, namely, 1,2-cis and 1,2-trans. This approach, as well as the ³J(CH) values and the analysis of the C-3′-endo?C-2′-endo equilibrium of the carbohydrate fragment of nucleosides, and circular dichroism (CD) data, provides important information on the conformation about the glycosidic bond. The magnitudes of ³J(C-4, H) are indicative of the position of attachment of the carbohydrate fragment to the heterocyclic base.     

SYNTHESIS OF THE C-DISACCHARIDE α-C(1→3)-L-FUCOPYRANOSIDE OF N-ACETYLGALACTOSAMINE[1]

Radical C-glycosidation of racemic 5-exo-benzeneselenyl-6-endo-chloro-3-methylidene-7-oxabicyclo[2.2.1]heptan-2-one ((±)-2) with α-acetobromofucose (3) provided a mixture of α-C-fucosides that were reduced with NaBH₄ to give two diastereomeric alcohols that were separated readily. One of them ((?)-6) was converted into (?)-methyl 2-acetamido-4-O-acetyl-2,3-dideoxy-3-C-(3′,4′,5′-tri-O-acetyl-2′,6′-anhydro-1′,7′-dideoxy-α-L-glycero-D-galacto-heptitol-1′-C-yl)-α -D-galactopyranuronate ((?)-11) and then into (?)-methyl 2-acetamido-2,3-dideoxy-3-C-(2′,6′-anhydro-1′,7′-dideoxy-α-L-glycero-D-galacto-heptitol-1′-C-yl)-β -D-galactopyranoside ((?)-1), a new α-C(1→3)-L-fucopyranoside of N-acetylgalactosamine. Its ¹H NMR data shows that this C-disaccharide (α-L-Fucp-(1→3)CH₂-β-D-GalNAc-OMe) adopts a major conformation in solution similar to that expected for the corresponding O-linked disaccharide, i.e., with antiperiplanar σ(C-3′,C-2′) and σ(C-1′,C-3) bonds.     

Etude Conformationnelle par Résonance Magnétique Nucléaire Protonique des Dérivés de la O-Isopropylidène-2′,3′ Adénosine

Conformational analysis using ¹H n.m.r. data (δ, ³J and NOE) has been carried out on several derivatives of 2′,3′,-O-isopropylideneadenosine bearing various substituents at positions C-5′, C-8 and N-6. Conformational modifications are assigned to specific interactions between the sugar and purine moieties and also to solvent effects.     

Carbon-13 nuclear magnetic resonance spectra of exo- and endo-2-norbornyltrimethyl-stannanes: Corrected assignments

The ¹³C NMR spectra of pure exo-2-norbornyltrimethylstannane and a mixture of the exo- and endo-isomers have been recorded. ¹H–¹³C polarization transfer spectra have been obtained and require the previously reported assignments for C-3 and C-4 in the exo-isomer to be reversed. The reported assignments for the endo-isomer are correct. The new assignment for C-4-exo [with J(¹¹⁹Sn,¹³C) vic=12 Hz, instead of the previously assigned J(vic)=23 Hz], has a very minor effect on the nature of the Karplus curve [for ³J(¹¹⁹Sn,¹³C)] generated previously.     

Détermination par RMN 1H et 13C des Couplages J(CH) et J(CC) dans des Monomères Precurseurs de Lignine: Vanilline,Férulate d'Ethyle et Alcool Coniférylique Sélectivement Enrichis en 2H et 13C

Some monomer model compounds of lignin have been selectively ²H and ¹³C labelled: vanillin, ethyl ferulate, coniferyl alcohol and ethyl hydrogen malonate. Deuterium isotope effects on the ¹³C chemical shifts in [formyl-²H]vanillin, [5-²H]vanillin and [α,α,5-²H₃]coniferyl alcohol made the unambiguous assignment of the aromatic ¹³C signals possible. Absolute ^1,2,3J(CC) values have been determined on ¹³C spectra of [formyl-¹³C]vanillin, and of ethyl ferulate and coniferyl alcohol in which the vinylic C-γ and C-β carbons were ¹³C enriched. It has been possible to measure ⁴J(C?O, C-4) in vanillin and ⁴J(C-γ, C-4) in ethyl ferulate. The determination of ^1,2,3,4J (CH) absolute values was done by means of gated decoupled ¹³C spectra of the non-labelled compounds. When second order effects made the use of this technique impossible we determined certain J(CH) values and their signs either by analysing the ¹H NMR spectra of ¹³C labelled coniferyl alcohol [²J(C-β, H-γ), ²J(C-β, H-α), ²J(C-γ, H-β), ³J(C-γ, H-α)] or by a double irradiation experiment on the 250 MHz ¹H NMR spectrum of ethyl [β-¹³C] ferulate [for ²J(C-β, H-γ)].     

1H- und 13C-NMR-Untersuchungen zur Struktur N-substituierter Tetrazole—Die Strukturen des N-Methoxycarbonyl-, N-Acetyl- und N-(Tri-n-butylstannyl)-tetrazols sowie Substituenteneffekte auf δ13C und 1J(CH)

The ¹H and ¹³C NMR spectra of several isomeric N-substituted tetrazoles have been investigated. ¹³C NMR is shown to be more useful for distinguishing between structural isomers of N-substituted tetrazoles except for those carrying electropositive substituents like SnBu₃. Correlations of δC-5 (inverse) and ¹J(C-5,H) with s?₁ found for 1-substituted tetrazole allowed the identification of the N SnBu₃ derivative as 1-(tri-n-butylstannyl)tetrazole. The phenyl carbon chemical shift difference ΔC′ = δC-3′-δC-2′ is insignificant for structure elucidation and conformational studies of N-substituted 5-phenyltetrazoles; ΔH′ from ¹H NMR spectra seems to be more useful.     

Selectively Deoxygenated Derivatives of β-Maltosyl-(1→4)-Trehalose as Biological Probes. II. the Synthesis of the 4- and 4′″-Monodeoxygenated Analogues

ABSTRACT

Two derivatives of β-maltosyl-(1→4)-trehalose monodeoxygenated at positions 4 or 4′″ have been synthesized in [2+2] block syntheses. After the preparation of precursors with only one free hydroxyl group the deoxy function was introduced by a Barton-McCombie reaction. Thus, glycosylation of 2,3,6-tri-O-benzyl-α-D-glucopyranosyl 2,3,6-tri-O-benzyl-α-D-glucopyranoside (4) with octa-O-acetyl-β-maltose (3) gave tetrasaccharide 5 with only one free hydroxyl group at the 4-position. The 4′-position of an allyl maltoside was available selectively after removal of a 4′,6′-cyclic acetal and selective benzoylation of the 6′-position. Reduction of this derivative 11 afforded allyl O-(2,3-di-O-acetyl-6-O-benzoyl-4-deoxy-α-D-glucopyranosyl)-(1→4)-2,3,6-tri-O-acetyl-β-D-glucopyranoside (14), which was deallylated, activated as an trichloroacetimidate, and coupled to 2,3-di-O-benzyl-4,6-O-benzylidene-α-D-glucopyranosyl 2′,3′,6′-tri-O-benzyl-α-D-glucopyranoside (20). Several compounds were fully characterized by ¹H NMR spectroscopy. Deprotection furnished the monodeoxygenated tetrasaccharides 9 and 23.     

The solid-phase synthesis of 2-5-linked oligoriboadenylates containing 8-bromoadenine

To increase the accessibility of 8-bromo-2′,5′-oligoadenylates, we developed a synthesis of 2′-5′-linked oligoriboadenylates containing varying numbers of 8-bromoadenosine residues based on the use of a CPG-LCA solid support and the phosphoramidite approach. Although N⁶benzoyl protection was satisfactory for incorporation of nonmodified adenine residues into 2′,5′-oligonucleotides, the effective incorporation of 8-bromoadenine into such 2′,5′-linked oligomers required use of a non acyl protecting group. Amidine protection of the purine exocyclic amino function proved compatible with all aspects of the phophoramidite approach and with the hydroxyl protection groups employed.     

Synthesis of some oxadiazole derivatives of d-mannose

The syntheses of 2-methyl-5-[1′,2′,3′,4′,5′-penta-O-benzoyl-D-manno-pentitol-1′-yl]-1,3,4-oxadiazole and 5-methyl-3-[1′,2′,3′,4′,5′-penta-O-benzoyl-D-manno-pentitol-1-′yl]-1,2,4-oxadiazole, as well as their intermediate products, are described. Their ¹H and ¹³C nmr and ms spectra are presented and their preferential conformation in solution are proposed.     

Darstellung intramolekular stabilisierter Diazaphosphorinan-Derivate mit der Trimethylethylendiamin- bzw. der Tetramethylguanidingruppe als Substituent am Phosphor: Studium intramolekularer Me2N → P-Wechselwirkungen

Formation of Intramolecularly Stabilized Diazaphosphorinane Derivatives with the Trimethylethylenediamine and the Tetramethylguanidine Group as Substituents at Phosphorus: Investigation of intramolecular Me₂N → P Interactions In the reaction of trimethylchlorophosphonium chloride 1 with N-trimethylsilyl-N′,N′,N″,N″-tetramethylguanidine 2 the expected guanidine-substituted trimethylphosphonium chloride 3 was formed, presumably via the ammonium chloride 3a which could not be isolated. By contrast, the reaction of the related chloromethyldimethylchlorophosphonium chloride 5 with N-trimethylsilyl-N,N′,N′-trimethylethylenediamine 6 and N-trimethylsilyl-N′,N′-dimethylethylene diamine, 7 , respectively, furnished in an unusual fashion six-membered heterocycles, the ammonium-phosphonium dichlorides 10 and 11 . Their formation involved cleavage of both the P? Cl and the C? Cl bond, followed by intramolecular C←N-acceptor-donor interaction. A similar C←N interaction was not observed in the reaction of 5 with 2 , and the acyclic product 12 was formed. The reaction of chloromethylmethylchlorophosphine 13 with the hydrogen peroxide/urea 1:1-adduct led to chloromethylmethylphosphinic acid 14 . Attempts at the reaction of 14 with 2 or with SOCl₂ were unsuccessful. The reaction products were characterized by ¹H-, ¹³C-, ³¹P- and, in two cases, by ¹⁵N-NMR-spectroscopy.     

Synthesis of spiro[1,4-benzothiazine-2,2′-pyrans] starting from methyl β-D-arabino-2-hexulopyranosonate

Dedicated to Professor Klaus Burger on the occasion of his 60th birthday Methyl β-D -arabono-2-hexulopyranosonate 1 has via the novel glycosyl donor 3 been transformed into the thiophenyl glycosides 4 and 5. Catalytic hydrogenation of the nitro compound 4 in alkaline solution led to spontaneous cyclization and deprotection to form the cyclic hydroxamic acid 7. The related lactams 8 and 9 were obtained from amine 5. The spiro[1,4-benzothiazine-2,2′-pyrans] 7–9 are the first representatives of a novel class of heterocycles structurally related to bioactive natural products. As shown by the values for J_3′,4′ and J_4′,5′ the glycosides 4, 5 and 6 adopt a ⁵C₂ conformation of the pyranoid ring whereas the 1,4-benzothiazine system in 7–9 forces a conformational change into the ²C₅ conformation.     

A study of the binding of manganese (II) with the sodium salts of nucleosides in aqueous solutions by the13C NMR method

The binding of manganese(II) with nucleosides — adenosine (A), guanosine (G), cytidine (C), and uridine (U) — in an alkaline D₂O solution has been investigated by the¹³C NMR method. It has been established that the structure of the paramagnetic Mn(II)—nucleoside complexes differs substantially in neutral and in alkaline media. The broadening of the resonance lines (C-2′, C-3′ > C-1′, C-4′ > C-5′) shows the localization of the Mn(II) in the C-2′ and C-3′ hydroxyls of the ribose in an alkaline medium. It has been shown for the case of U that the degree of complex-formation depends on the pH of the solution. It is assumed that the nucleoside forms intramolecular complexes (I) with Mn(OH)₂.     

13C?13C coupling constants in derivatives of trans-stilbene and tetraphenylethylene. Determination of relative signs II

Magnitudes and signs of ¹³C? ¹³C coupling constants in compounds of the type Ph¹³CR¹R²? ¹³CR¹R²Ph have been determined and the results are discussed in a broader context. Two types of coupling constants, J(C-i, C-α) and J(C-i, C-β), between aromatic carbon atoms and the benzylic carbons, probably with different coupling mechanisms, are considered. Whereas ²J(C-2, C-α) are always found positive, ²J(C-1, C-β) in the present compounds are found to be negative or about zero. ³J(C-3, C-α) has the same sign as ²J(C-2, C-α). A ⁴J and a ⁵J were observed in trans-stilbene.