Spin-decoupling Experiments Research Articles

Cis- and trans-1-[3-(Hydroxymethyl)-1,4-dioxepan-5-yl]pyrimidines: a new nucleoside prototype with a seven-membered moiety

We synthesized nucleoside analogues with a seven-membered moiety as the carbohydrate fragment mimicking the upper part of biologically active natural and synthetic nucleosides, starting from 3-iodomethyl-5-methoxy-1,4-dioxepane. The reaction sequence involved the substitution of the iodine atom by the acetoxy group, condensation with the nucleobases and subsequent saponification. The cis/trans mixtures of the target compounds were separated by reversed-phase preparative HPLC. The relative configurations of each of the hydrogen atoms of the cis and trans newly synthesized compounds were determined by spin decoupling, 2D NOESY and COSY experiments. None of this series showed activity in antiviral tests in cell cultures.

Rearranged abietane diterpenes from Salvia limbata

Six new rearranged abietane diterpenes were isolated from the roots of Salvia limbata. Their structures were established by 1D and 2D NMR techniques including spin decoupling, COSY, APT, HETCOR and COLOC experiments

Rearrangements of 2,6-diaryl-3,7-dioxabicyclo[3.3.0]octane lignans reactions of paulownin and wodeshiol with triethylsilane and BF 3-etherate

Paulownin on treatment with triethylsilane and BF 3-etherate reacts in a similar manner to gmelinol, giving an aryltetralin as the product. In contrast, wodeshiol under the same conditions rearranges to two isomeric tetrahydropyran derivatives, the structures of which have been deduced on the basis of their 1H and 13C n.m.r. spectra, including NOE and spin decoupling experiments.

A lupine alkaloid from Leontice leontopetalum

Abstract Leontice leontopetalum from Jordan has yielded the new lupine alkaloid, 3α-hydroxylupanine. Its structure was confirmed by the use of mono- and bi-dimensional NMR techniques (GASPE, DEPT, homonuclear spindecoupling experiments, 1 H/ 1 H-COSY, 1 H/ 13 C-COSY), linked scan measurements and by chemical transformation. The isolation of 13α-hydroxylupanine and isolupanine are also described and their 1 H and 13 C NMR spectral data have been reinvestigated employing GASPE, DEPT, HMQC and HOHAHA experiments.

Isolation and two-dimensional 1H-NMR of peptide [1–24] of dog serum albumin and studies of its complexation with copper and nickel by NMR and CD spectroscopy

The NH 2-terminal peptide fragment [1–24] of dog serum albumin was obtained by controlled peptic digestion of the protein. The peptide was purified to homogeneity by gel filtration and ion-exchange chromatography. The NMR assignments of the protons of the individual amino acid residues were made by using two-dimensional correlation matrix, spin-decoupling experiments and analysis of the titration curves. The polypeptide itself has a random-coil conformation. There is a conformational change as a function of pH, but it does not arise from any direct involvement of the amino acid side chains. Complexation of the peptide fragment with Ni(II) and Cu(II) has been investigated by NMR and CD. The Ni(II) complex is in slow exchange with the free ligand on the NMR time scale. The complexation involves the α-NH 2, three deprotonated amide nitrogens of Ala-2, Tyr-3 and Lys-4 residues. The phenolate oxygen of Tyr-3 is not involved in the metal binding; however, an interaction between the aromatic ring and the metal ion is likely. The CD results of Cu(II)-binding to this peptide suggest that the complexation takes place from the terminal NH 2 and step by step to three deprotonated amide nitrogens. There is no major conformational change of the peptide fragment upon complexation.

Depolymerization of pectin with diazomethane in the presence of a small proportion of phosphate buffer

Treatment of pectin with diazomethane in diethyl ether in the presence of a small proportion of phosphate buffer resulted in considerable depolymerization of the polysaccharide chain and concomitant methylation of the hydroxyl groups. A mixture of the depolymerized products was fractionated by gel-filtration on a Toyopearl HW-40S column to give di- and tri-saccharide fractions, which were subsequently permethylated with diazomethane-boron trifluoride etherate. The resulting permethylated di- and tri-saccharide fractions were separated into two di- and four tri-sacchraides by reversed phase l.c., followed by adsorption l.c. The 1H-n.m.r. spectra of the isolated oligosacchraides were studied by homonuclear, spin-decoupling experiments, COSY-45 two-dimensional homonuclear correlation experiments, two-dimensional J-resolved methods, and two-dimensional 13C 1H correlation experiments. The structures ( 1 and 2) for the two disaccharides, and those ( 3 and 4) for two of the four trisaccharides were determined. The structures 5 and 6 for the remaining trisaccharides were tentatively deduced from their 1H-n.m.r. spectral data.

N.M.R. studies of the disulphated disaccharide obtained by degradation of bovine lung heparin with nitrous acid

The disulphated disaccharide IdoA(2SO 3)—anManOH(6SO 3) was prepared from bovine lung heparin by treatment with nitrous acid followed by borohydride reduction. The 1H- (400 MHz) and 13C-n.m.r. (100 MHz) spectra of this disaccharide derivative have been assigned completely using homonuclear spin-decoupling experiments, 13C 1H correlations, and a COSY-45 two-dimensional homonuclear correlation experiment. The 3J H,H values show that the IdoA(2SO 3) residue exists in a single conformation throughout the temperature range 20–90°.

Structure of Alamethicin in solution: One- and two-dimensional 1H nuclear magnetic resonance studies at 500 MHz

We report here the 500 MHz 1H nuclear magnetic resonance spectra of Alamethicin, an icosapeptide antibiotic isolated from Trichoderma viride, in methanol, water and methanol/water mixtures. At this frequency, resonances from all the protons are well-resolved in methanol and may be assigned unambiguously. Spectral assignments were made using two-dimensional spin-echo correlated spectroscopy and by spin-decoupling experiments. The amide coupling constants (JNH-alpha CH) facilitated conformational predictions, which were confirmed in part by two-dimensional nuclear Overhauser experiments. On the basis of these data, we propose a secondary structure for Alamethicin that is alpha-helical toward the N terminus and extended beta-sheet at the C-terminal end. This structure is consistent with earlier circular dichroism measurements (McMullen et al., 1971), infrared attenuated total reflection spectroscopy studies (Fringeli & Fringeli, 1979) and proton exchange data (Davis & Gisin, 1981). The proposed structure is a tightly bound dimer, wherein the beta-sheet is stabilized by intermolecular hydrogen-bonds between opposing molecules. An interesting feature of this structure is that it exhibits both a hydrophobic and a hydrophilic surface. This highly amphiphilic nature of the dimer structure may account for the extensive further aggregation of Alamethicin in water. The 1H n.m.r. spectrum of Alamethicin in water is broad, suggesting extensive association. However, spectral assignments and amide coupling constant measurements in water, which were accomplished by titration of methanolic solution of Alamethicin by water, revealed no gross changes in the basic secondary structure of the molecule.

Chemical shift changes in the1H nuclear magnetic resonance spectrum of β-D-arabinose induced by boron(III) oxide

The 1H n.m.r. spectrum of β-D-arabinose was measured at 89.6 MHz in the presence of boron(III) oxide. The boron(III) oxide produces remarkable chemical shift changes in hydroxy proton signals and the signals of all methine and methylene groups in the β-D-arabinose dissolved in (CD3)2SO. The assignments of the spectrum of β-D-arabinose with 2 mol. equiv. of boron(III) oxide were determined by spin-decoupling experiments.

The antarctic lichens: 1—The stereochemistry of 7β‐acetoxy‐22‐hydroxyhopane from Pseudocyphellaria freycinettii, indigenous to S. Georgia

AbstractFrom differential spin decoupling and nuclear Overhauser enhancement experiments, the 400 MHz 1H NMR spectrum of the triterpene 7β‐acetoxy‐22‐hydroxyhopane is interpreted to establish the α‐configuration of the side‐chain at C‐21.

Complete assignment of the 1H NMR spectrum of the aromatic residues of lysozyme.

Assignment of the nuclear magnetic resonance (NMR) spectrum of the 59 non-exchangeable protons of the 13 aromatic amino acid residues of lysozyme has been completed using a combination of selective spin decoupling and nuclear Overhauser experiments. The experimental chemical shift data were used to simulate the aromatic region of the NMR spectrum at 300 MHz and at 470 MHz. Excellent agreement with the experimental spectra was obtained and the simulations permitted more accurate chemical shift values and resonance linewidths to be obtained. The current set of assignments is compared with those of the assignments made previously. Evidence for the motional behaviour of the aromatic amino acid side chains is presented.

15-Acetoxycostunolide from Magnolia sieboldii

A new germacranolide isolated from M. sieboldii was shown to be 15-acetoxycostunolide by spectroscopic and chemical methods. 1H NMR spin decoupling and NOE experiments in the presence of a lanthanide shift reagent were used for structure elucidation.

Isolation and characterization of pyrimidine-psoralen photoadducts from DNA

We have examined the photoadducts of 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) and native DNA. Five nucleoside-HMT monoaddition products have been isolated and characterized, corresponding to three deoxythymidine-HMT and two deoxyuridine (derived from deoxycytidine)-HMT adducts. Structural assignments are based on high resolution mass spectrometry and /sup 1/H NMR studies, including homonuclear spin decoupling and nuclear Overhauser effect (NOE) experiments. The results of this study indicate that (1) a limited number of nucleoside-psoralen adducts are formed with native, double-stranded DNA, and (2) the sterochemistry of the adducts is apparently determined by the geometry of the noncovalent intercalative complex formed by HMT and DNA prior to irradiation. 8 figures, 8 tables.

Synthesis and crystal structure of the trimetal compound [Pt3(C2H4)(C8H8)2(1,5-C8H12)2]: a complex of platinum(0) and platinum(II)

Bis(cyclo-octa-1,5-diene)platinum, dissolved in ethylene-saturated diethyl ether, reacts with cyclo-octatetraene to give the triplatinum complex [Pt3(C2H4)(C8H8)2(1,5-C8H12)2], which has been characterised by a single-crystal X-ray diffraction study. Crystals of the triplatinum compound are monoclinic, space group C2/c, with Z= 4 in a unit cell of dimensions a= 16.370(17), b= 7.465(5), c= 24.603(37)A, β= 102.55(10)°. The structure has been solved by heavy-atom methods and refined by least squares to R 0.062 (R′ 0.062) for 3 341 independent diffracted intensities measured at 200 K. The molecule lies astride a crystallographic two-fold axis, with the trimetal system being significantly non-linear [Pt(2)–Pt(1)–Pt(2′) 158°]. The Pt–Pt separations of 3.166(1)A indicate little or no direct metal–metal bonding. Two cyclo-octa-1,5-diene ligands, in their usual tub-like configuration, are η4-co-ordinated to Pt(2) and Pt(2′). The Pt(1)–Pt(2) and Pt(1)–Pt(2′) vectors are bridged by two C8H8 ligands which employ four adjacent carbon atoms for bonding to the metal atoms. Of these carbon atoms, the central pair form a CC bond η2-co-ordinated to Pt(1) while the outer two are attached to Pt(2)[or Pt(2′)] by σ bonds. The central metal atom Pt(1) is also bonded to an ethylene molecule so that it is in a distorted trigonal configuration, in contrast to Pt(2) and Pt(2′) which have an essentially square-planar environment comprising the two σ bonds from one C8H8 ligand and the CC bonds of a C8H12 ring. Hence Pt(1) can be regarded as platinum (0), and the Pt(2) and Pt(2′) atoms as being in a PtII oxidation state. From variable-temperature 1H n.m.r. studies it was shown that the compound undergoes dynamic behaviour in solution. The mechanism is discussed, and the spectrum analysed by spin-decoupling experiments. The 13C n.m.r. spectrum is also reported.

The isomeric biliverdins from ring-cleavage of deuteroporphyrin-IX

Summary Treatment of zinc(II) deuteroporphyrin-IX dimethyl ester with thallium(III) trifluoroacetate, followed by acid treatment, affords the four isomeric oxophlorins (oxyporphyrins) in a reaction which is considerably more easy to control than the traditional method involving “coupled oxidation” of the corresponding hemin. The oxophlorins, obtained in very high yield, are chromatographically separable on a preparative scale. Using nuclear Overhauser enhancement and NMR spin-decoupling experiments, the isomeric deuterobiliverdins and meso-acetoxyporphyrins derived from the isomerically pure oxophlorins are assigned definitive structures. This work suggests that the original assignments of the β- and δ- deuterobiliverdins, made on the basis of coupled oxidation of deuterohemin-reconstituted hemoglobin, should be reversed. Implications for heme orientation in deuterohemin-reconstituted hemoglobin are discussed.

Individual assignments of the heme resonances in the 360 MHz 1H NMR spectra of cytochrome c-557 from Crithidia oncopelti

With the use of nuclear Overhauser effects, spin decoupling and saturation transfer experiments individual assignments for numerous resonances of the heme group in the 360 MHz 1H NMR spectra of reduced and oxidized cytochrome c-557 from Crithidia oncopelli were obtained. These data provide direct evidence that the heme substituent in position 2 is a vinyl group. They further show that in spite of the different covalent structures of the heme groups the heme crevice and the electronic heme structure in the oxidized state are nearly identical in cytochrome c-557 and in mammalian cytochromes c.

Phytochrome Models, I. Isolation, Characterization, and Solution Conformation of Biliverdin Dimethyl Ester and Its XIIIα Isomer

AbstractBiliverdin dimethyl ester (1b; IXα) and its XIIIα isomer 2b have been isolated on a preparative scale after esterification of an isomeric mixture obtained by oxidation of bilirubin. Both isomers readily form solid solutions. The substitution patterns and the predominant helical „all‐Z”︁ configuration, „all‐syn”︁ conformation of 1b and 2b are assigned on the basis of an 1H‐NMR study including spin decoupling and nuclear Overhauser effect experiments. The electronic absorption spectra of the two isomers differ significantly. The ethyl (S)‐(‐)‐lactate‐induced circular dichroism of 1b and 2b in the long and short wavelength regions is similar to that found for biliverdin‐peptide complexes.

A nuclear-magnetic-resonance study of the globular structure of the H5 histone.

The structure of the globular region of the chicken erythrocyte H5 histone has been studied by 270-MHz proton magnetic resonance. The aromatic resonances have been partially assigned by a combination of selective deuteration and iodination with the nuclear magnetic resonance spectroscopy. Detailed titration studies have revealed interactions between residues in the structure. A technique involving the measurement of small nuclear Overhauser effects has enabled the assignment of the aromatic residues causing the perturbation of the ring-current-shifted methyl resonances occurring in the upfield region of the spectrum. Spin-decoupling experiments on these peaks has enabled a partial assignment of shifted methyl resonances. The results support the notion that the histone H5 globular structure is different from that of the homologous histone H1 molecule.

Individual assignments of the methyl resonances in the proton nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor

In earlier work the resonances of the 20 methyl groups in the basic pancreatic trypsin inhibitor (BPTI) had been identified in the 360-MHz 1H nuclear magnetic resonance (NMR) spectra and most of the methyl lines had from spin-decoupling experiments been assigned to the different types of amino acid residues. The assignments to the different amino acid types were now completed by studies of the saturation transfer between the denatured and the globular forms of the inhibitor and by spin-decoupling experiments in nuclear Overhauser enhancement (NOE) difference spectra. These distinguished between the methyl resonances of Ala and Thr. Furthermore, for most of the methyl resonances, individual assignments to specific residues in the amino acid sequence were obtained from measurements of intramolecular proton-proton NOE's, use of lanthanide NMR shift and relaxation probes, and comparative studies of various chemically modified forms of BPTI. These data provide the basis for individual assignments of the methyl 13C NMR lines in BPTI and for detailed investigations of the relations between the spatial structure of the protein and the chemical shifts of the methyl groups. The methyl groups in BPTI are of particular interest since they are located almost exclusively on the surface of the protein and thus represent potential natural NMR probes for studies of the protein-protein interactions in the complexes formed between BPTI and a variety of proteases.

A nuclear-magnetic-resonance study of the globular structure of the H1 histone.

The globular structure of the H1 histone has been studied by 1H NMR, as an aid to elucidating its mode of action, and also as a model small protein molecule for investigating the capabilities of NMR for gaining information about the tertiary folding when the structure has not been determined by other techniques. Guanidylation of the lysine residues does not effect the capability of the peptide chain to fold into the native globular structure, suggesting that the lysine residues are on the surface of the structure. Partial assignment has been made of some of the ring‐current‐shifted resonances (i.e. resonances from methyl groups of apolar residues which are shifted by their proximity to the magnetic fields of aromatic rings) by a combination of spin‐decoupling experiments and theoretical ring‐current‐shift stimulations. Substitution of the tyrosine residue of histone H1 considerably weakens the globular structure, and observation of specific changes in the perturbed methyl region of the spectra on substitution indicates the aromatic residues giving rise to ring‐current perturbation of specific peaks in the spectrum. Interproton Overhauser effects are demonstrated, arising from throughspace dipole interaction between protons of the aromatic residues and methyl residues, the resonances of which are perturbed by close proximity to the aromatic rings. The results of these experiments confirm the assignments made from the results of the tyrosine modification experiments.