Dimensional NMR Spectroscopy Research Articles

Structural and conformational analysis of 2-triphenylphosphoranylidene succinic acid derivatives by1H,13C and31P one and two dimensional NMR spectroscopy and molecular modelling

The structure and conformation of 2-triphenylphosphoranylidenesuccinic acid derivatives have been studied by 1H, 13C and 31P NMR spectroscopy, in various solvents and at variable temperatures. In 2-triphenylphosphoranylidenesuccinic anhydride (1) the conformation is constrained but in the corresponding monoethyl (2) and the diethyl (3) esters there is an anticlinal relationship between the phosphorus and hydrogens on C-3 and signals of Z and E isomers were observed with the diethyl ester 3 in solvent-dependent ratios based on 1H, 13C and 31P resonances. Similar results were obtained with the diethyl ester of the 3-methyl derivative 4. Protonation (deuteronation) of 2 and 3 changes their conformation and P–H couplings. The NMR evidence on conformations of the phosphoranylidenesuccinic acid esters is consistent with T1 relaxation times and results of molecular modelling.

Site selective bis-intercalation of a homodimeric thiazole orange dye in DNA oligonucleotides.

We have used one and two dimensional 1H NMR spectroscopy to characterize the binding of a homodimeric thiazole orange dye, 1,1'-(4,4,8,8-tetramethyl-4,8-diaza-undecamethylene)-bis-4- (3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)-quinolin ium tetraiodide (TOTO), to various double stranded DNA oligonucleotides. TOTO binds strongly to all the oligonucleotides used, but usually more than one complex is observed and exchange between different binding sites broadens the lines in the NMR spectra. Complete precipitation occurs when TOTO is bound to small oligonucleotides. Binding to larger oligonucleotides occurs by bis-intercalation. The 1:1 complex of TOTO with the oligonucleotide d(CCGACTGATGC):d (GCATCAGTCGG) gave only one complex that was shown to be a bis-intercalation in the CTGA:TCAG binding site. The binding to this site was also characterized by studying the TOTO complex with the d(CCGCTGAGC):d(GCTCAGCGG) oligonucleotide. NOE connectivities and molecular modelling were used to characterize the complex. The 1:1 complex of TOTO with the oligonucleotide d(CCGCTAGCG):d(CGCTAGCGG) containing a CTAG:CTAG binding site was similarly characterized by NMR. It was concluded that the binding of TOTO to larger oligonucleotides is site selective with CTAG:CTAG as the preferred binding site.

Secondary structures in β-casein peptide 1–42: a two dimensional nuclear magnetic resonance study

Two dimensional NMR spectroscopy was used to study the structure of a peptide composed of the N-terminal 42 amino acid residues of beta-casein. The peptide was obtained by enzymic cleavage using endoproteinase Asp-N. Complete sequence-specific 1H NMR assignment was performed for the peptide at three Ca2+ concentrations (0, 22 and 37 mM). The NMR results show that the peptide was highly flexible and adopted multiple conformations. No stable secondary structures were present; however, the peptide had some regions with non-random structure. The region between residues Leu16 and Asn27 adopted conformations with an increased contribution of alpha-helical structure, a so-called nascent helix. Two regions, Glu11-SerP15 and Lys29-Phe33 showed an increased population of conformations with extended structures. Addition of Ca2+ induced chemical shift changes for the backbone amide protons, especially around the phosphoserine region and around the suggested alpha-helical structure, indicating that the addition of Ca2+ stabilized the structure already present in the apo form of the peptide.

Yellow mustard mucilage: chemical structure and rheological properties

Water-soluble yellow mustard ( Sinapis alba L.) mucilage was found to exhibit pronounced shear thinning behaviour at polymer concentrations between 0.3 and 2.0% at 22.0°C. Isolation and fractionation by hexadecyltrimethylammonium bromide (CTAB) precipitation and ion exchange chromatography produced a number of polysaccharide fractions. This permitted a closer examination of both structural features and rheological properties of yellow mustard polysaccharides. CTAB-precipitated fraction (WSCP) was found to be the major component which contributed more to the weak gel-like properties of the water-soluble yellow mustard polysaccharides than the CTAB soluble fraction (WSCS). Of the ten fractions separated from WSCP and WSCS by ion exchange chromatography, only two fractions from the WSCP (WSCP-I and WSCP-III) and one fraction from WSCS (WSCS-I) appeared responsible for the pronounced shear thinning behaviour of water-soluble yellow mustard mucilage. WSCP-I and WSCS-I were mainly composed of 1, 4-linked β- D-glucans as revealed by methylation analysis and/or NMR spectroscopy. WSCP-III was identified as a pectic polysaccharide containing 1, 6-linked galactose, 1, 2-linked and 1, 2, 4-linked rhamnose, 1, 4-linked galacturonic acid and non-reducing end glucuronic acid. Partial structure of WSCP-III was elucidated by one and two dimensional NMR spectroscopy of the oligosaccharides isolated from the partial hydrolysates.

One dimensional high resolution 1H NMR spectroscopy of human bile: lipid-derived resonance shifts

One dimensional high resolution 1H NMR spectroscopy of human bile: lipid-derived resonance shifts

Mono- versus dinuclear cobalt complexes of a binucleating Schiff base ligand

The Schiff base ligand 2,6-bis{2-[(3,5-dimethyl-2-hydroxyphenyl)imino]-methyl}-4-methylphenol (H 3L), when reacted with COCl 2 forms the monocobaltic complex, HLCoCl ( 5). This diamagnetic complex is readily characterized by two- dimensional 1H NMR spectroscopy. Complex 5 reacts with a second cobalt ion in the presence of sodium benzoate to form LCo IICo III(Cl)(O 2CC 6H 5). Comparisons are made between this complex and the dicobaltic complex of the analogous polypodal ligand 2, 6-bis{[(2-hydroxyphenyl)(2-pyridylmethyl)amino]-methyl}-4-methylphenol.

Structural studies on sulfated oligosaccharides derived from the carbohydrate-protein linkage region of chondroitin 6-sulfate proteoglycans of shark cartilage. II. Seven compounds containing 2 or 3 sulfate residues.

Shark cartilage proteoglycans bear predominantly chondroitin 6-sulfate. After exhaustive protease digestion, reductive beta-elimination and subsequent chondroitinase ABC digestion, 13 hexasaccharide alditols were obtained from the carbohydrate-protein linkage region and six of them contain 0 or 1 sulfate and/or 1 phosphate residue (Sugahara, K., Ohi, Y., Harada, T., de Waard, P., and Vliegenthart, J. F. G. (1992) J. Biol. Chem. 267, 6027-6035). The other seven compounds, which represent approximately 60% of the isolated linkage hexasaccharides, were analyzed by chondroitinase ACII digestion in conjunction with high performance liquid chromatography and by 500-MHz one- and two dimensional 1H NMR spectroscopy. All seven compounds have the following conventional structure in common. [formula: see text] Two disulfated compounds have an O-sulfate on C-6 of the Gal-2 residue attached to xylitol in combination with an O-sulfate on C-4 or on C-6 of the GalNAc residue. The third disulfated compound has O-sulfate on C-6 of Gal-2, and also on C-6 of Gal-3. Two of the trisulfated compounds also have O-sulfate on C-6 of both Gal-2 and Gal-3 with in addition sulfate on C-6 or C-4 of GalNAc. The other two trisulfated compounds have O-sulfate on C-6 of Gal-2 and on C-4 of Gal-3 in conjunction with sulfate on C-6 or C-4 of GalNAc.

Solution conformation of an oligonucleotide containing a urea deoxyribose residue in front of a thymine.

Urea residues are produced by ionizing radiation on thymine residues in DNA. We have studied an oligodeoxynucleotide containing a thymine opposite the urea residue, by one and two dimensional NMR spectroscopy. The urea deoxyribose exists as two isomers with respect to the orientation about the peptide bond. For the trans isomer we find that the thymine and urea site are positioned within the helix and are probably hydrogen bonded. The oligonucleotide adopts a globally B form structure although conformational changes are observed around the mismatch site. A minor species is observed, in which the urea deoxyribose and the opposite base adopt an extrahelical position and this corresponds to the isomer cis for the peptide bond.

Conformational analysis of receptor selective tachykinin analogs: senktide and septide.

The conformational behavior in solution of two receptor selective tachykinin agonists, senktide (succinyl-D-F-MeF-G-L-M-NH2) and septide (pQ-F-F-P-L-M-NH2) is described. Two dimensional cross relaxation NMR spectroscopy is used together with coupling constant data to obtain interproton distance constraints. These results are used in conjunction with semi-empirical energy computations to indicate favorable conformations. Senktide is found to have a high degree of conformational order which is attributed to rotational restriction associated with the N-methylation of phenylalanine. The lowest energy conformation in accord with the experimental interproton distances contains a beta-turn. Interproton distances indicate that septide exists as a random coil or in an extended chain conformation. Energy computations suggest that septide is primarily an extended chain with internal reorientation restricted by the proline residue. These results may be related to the selectivity of these peptides for different receptors, in that the analogs, with conformations more stable than tachykinins, are more receptor selective.

One and Two Dimensional NMR Spectroscopy. Von Atta‐ur‐Rahman. Elsevier, Amsterdam 1989. XIX, 578 S., geb. HFl. 355.00.‐ISBN 0‐444‐87316‐3

Angewandte ChemieVolume 103, Issue 2 p. 221-222 Neue Bücher One and Two Dimensional NMR Spectroscopy. Von Atta-ur-Rahman. Elsevier, Amsterdam 1989. XIX, 578 S., geb. HFl. 355.00.-ISBN 0-444-87316-3 Ad Bax, National Institutes of Health, Bethesda, MD 20205 (USA)Search for more papers by this author Ad Bax, National Institutes of Health, Bethesda, MD 20205 (USA)Search for more papers by this author First published: Februar 1991 https://doi.org/10.1002/ange.19911030235AboutPDF ToolsRequest permissionAdd to favorites ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume103, Issue2Februar 1991Pages 221-222 This is the German version of Angewandte Chemie. Note for articles published since 1962: Do not cite this version alone. Take me to the International Edition version with citable page numbers, DOI, and citation export. We apologize for the inconvenience. RelatedInformation

Book Review: One and Two Dimensional NMR Spectroscopy. By Atta‐ur‐Rahman

Book Review: One and Two Dimensional NMR Spectroscopy. By Atta‐ur‐Rahman

Structure of a streptococcal adhesin carbohydrate receptor.

Interactions between complementary protein and carbohydrate structures on different genera of human oral bacteria have been implicated in the formation of dental plaque. The carbohydrate receptor on Streptococcus sanguis H1 (one of the primary colonizing species) that is specific for the adhesin on Capnocytophaga ochracea ATCC 33596 (a secondary colonizer) has been isolated from the streptococcal cell wall, purified, and structurally characterized. The hexasaccharide repeating unit of the polysaccharide was purified by reverse-phase, amino-bonded silica, and gel permeation high performance liquid chromatography. Earlier studies established that the repeating unit was a hexasaccharide composed of rhamnose, galactose, and glucose in the ration of 2:3:1, respectively. In the present study, determination of absolute configuration by gas chromatography of the trimethylsilyl (+)-2-butyl glycosides revealed that the rhamnose residues were of the L configuration while the hexoses were all D. 252Californium plasma desorption mass spectrometry of the native, the acetylated and the reduced and acetylated hexasaccharide determined that the molecular mass of the native hexasaccharide was 959, and that the 2 rhamnose residues were linked to each other at the nonreducing terminus of the linear molecule. Methylation analysis revealed the positions of the glycosidic linkages in the hexasaccharide and showed that a galactose residue was present at the reducing end. The structural characterization of the hexasaccharide was completed by one and two dimensional 1H and 13C NMR spectroscopy. Complete 1H and 13C assignments for each glycosyl residue were established by two-dimensional (1H,1H) correlation spectroscopy, homonuclear Hartmann-Hahn, and (13C,1H) correlation experiments. The configurations of the glycosidic linkages were inferred from the chemical shifts and coupling constants of the anomeric 1H and 13C resonances. The sequence of the glycosyl residues was determined by a heteronuclear multiple bond correlation experiment. These data show that the structure of the hexasaccharide repeating unit derived from the cell wall polysaccharide of S. sanguis H1 is: alpha-L-Rhap-(1----2)-alpha-L-Rhap-(1----3)-alpha-D-Galp- (1----3)-beta-D-Galp-(1----4)-beta-D-Glcp-(1----3)-alpha/beta-D-Gal.

Synthesis and 2D NMR spectra of α-cynichrodenyl-α-ferrocenylmethylium tetrafluoroborate

Reduction of [η 5-(ferrocenoyl)cyclopentadienyl]dicarbonylnitrosylchromium (hereafter called cynichrodenylferrocenylketone) ( 1) with sodium borohydride gives cynichrodenylferrocenyl carbinol ( 5), whereas reduction with lithium aluminum hydride/ alluminum chloride leads to cynichrodenylferrocenylmethane ( 6). Protonation of 5 with fluoroboric acid produces α-cynichrodenyl-α-ferrocenylmethylium tetrafluoroborate ( 4), a new dimetallocenyl-stabilized carbonium ion. The diastereotopism of 1H and 13C nuclei was observed in both of 4 and 5. The chemical shifts of H(2–5) protons and C(2–5) carbons in 1H and 13C NMR spectra respectively have been assigned using two dimensional NMR spectroscopy.

One and two dimensional NMR spectroscopy

One and two dimensional NMR spectroscopy

An antimicrobial alkaloid from Ficus septica

A methanolic extract of Ficus septica leaves displayed intense antibacterial and antifungal activities. Bioactivity-guided fractionation with TLC bioautography led to the isolation of two indolizidine alkaloids, the novel ficuseptine, 4,6- bis-(4-methoxyphenyl)- 1,2,3-trihydroindolizidinium chloride, and antofine. The structure of ficuseptine was determined from mass spectrometry and extensive one and two dimensional NMR spectroscopy. Complete 1H and 13C NMR assignments for antofine are reported.

Observation of arginyl-deoxyoligonucleotide interactions in TaqI endonuclease by detection of specific 1H NMR signals from 140kD [Nη1, Nη2, 15N Arg] TaqI/oligomer complexes

Proton and nitrogen signals of the guanidinium amines in [Nη1, Nη2 15N Arg] TaqI endonuclease were observed using isotope filtered experiments and proton detected 1H{ 15N} heterocorrelated two dimensional NMR spectroscopy. These rapidly exchanging protons could be detected in the free enzyme only at pH 4.5; at pH 8.5, no signals were measured after extensive signal averaging. Addition of deoxyribonucleotide oligomers resulted in the appearance of two groups of signals at about 6.8 and 7.5 ppm. Since these signals are independent of the presence of cognate sequence or Mg 2+, it is assumed they represent nonspecific arginyl-DNA interactions. This labeling/NMR approach provides a new method for investigating the role of arginine in protein-DNA interactions.

Isolation and identification of sialylcompounds from hemofiltrate

Hemofiltrate of patients with end stage renal disease is a source of sialyl compounds of unusual composition which accumulate in uremia. The large volumes involved (20–30l), are concentrated and desalted by modified reverse osmosis using membranes with a nominal cut-off of 500 D. The transport of the individual solutes during this process is monitored by reversed-phase HPLC of the permeates and retentates, respectively. By a combination of size-exclusion and ion-exchange chromatography 11 sialyl compounds are isolated preparatively. All structures have been determined using one and two dimensional NMR spectroscopy, enzymatic degradation and FAB mass spectrometry.

Phosphoramidate Analogs of Dinucleotides: Synthesis and1H Assignment by Two Dimensional NMR Spectroscopy (1H,1H-COSY)

Abstract The synthesis of several dinucleoside phosphate derivatives which are linked by phosphoramidate bonds 3′-OP(O)NH-5′ are described. One of these dimer units can be used in automated solid phase DNA synthesis by the phosphoramidite procedure. In order to study the conformational change which is induced on substituting O-P-0 against O-P-N we have also p-repared the fully deprotected dimer analog. The constitution of the dimer units were confirmed by means of 2D-300MHZ homonuclear chemical shift correlation spectroscopy (1H,1H-COSY).

Investigation of the solution structures and mobility of oxidised and reduced cytochrome b5 by 2D NMR spectroscopy

Two dimensional 1H NMR spectroscopy is used to examine the structure and mobility of cytochrome b 5 in solution. The assignment of many residues and the interpretation of nuclear Overhauser effects (NOEs) in both redox states allow definition of secondary structural elements. Comparison with X-ray diffraction data shows that differences between crystal and solution structures are small. The dynamics of the protein are examined and the protein is shown to be more mobile than cytochrome c. The relationship of the structure and dynamics to the electron transfer function of cytochrome b 5 is discussed.

Diversity of the gramicidin a spatial structure: two-dimensional 1H nmr study in solution

Theoretical consideration reveals a unique relationship between NMR spectral parameters and possible types of the gramididin A spatial structure. By means of two dimensional NMR spectroscopy four distinct species were detected simultaneously in ethanol solution. Comparison of experimental data and theoretical conclusions demonstrates that species 1 and 2 are left-handed parallel double helices ▪ differing in relative arrangement of the two polypeptide chains within the dimers, species 3 is left-handed antiparallel double helix ▪, and species 4 is a mirror image of species 1, i.e. right-handed parallel double helix ▪. The results are compared with those on spatial structures of the peptide in complex with cesium (right-handed antiparallel double helix ▪) and of the gramicidin A transmembrane ionchannel (N-terminal to N-terminal single-stranded dimer ▪).