One-dimensional NMR Spectroscopy Research Articles

The composition and structure of polyvinyl butyral furfural: NMR study

With the use of 1H NMR, 13C NMR and two-dimensional NMR spectroscopy, the composition and structure of polyvinyl butyral furfural samples obtained at different stages of poly(vinyl alcohol) acetalization have been determined. The structure of low-molecular-mass and oligomer admixtures that may be formed in the course of synthesis of the copolymer or during its dissolution in alcohol has been estimated via one-dimensional and two-dimensional diffusion NMR spectroscopy.

Hygrocins C–G, Cytotoxic Naphthoquinone Ansamycins from gdmAI-Disrupted Streptomyces sp. LZ35

Six hygrocins, polyketides of ansamycin class, were isolated from the gdmAI-disrupted Streptomyces sp. LZ35. The planar structure of hygrocins C-E (1-3) was determined by one-dimensional and two-dimensional NMR spectroscopy and high-resolution mass spectrometry. They are derivatives of hygrocin A but differ in the configuration at C-2 and the orientation of the C-3,4 double bond. Hygrocin F(4) and G(5) were shown to be isomers of hygrocin C (1) and B (6), respectively, due to the different alkyl oxygen participating in the macrolide ester linkage. Hygrocins C, D, and F were found to be toxic to human breast cancer MDA-MB-431 cells (IC50 = 0.5, 3.0, and 3.3 μM, respectively) and prostate cancer PC3 cells (IC50 = 1.9, 5.0, and 4.5 μM, respectively), while hygrocins B, E, and G were inactive.

1H and 13C NMR investigation of 20‐hydroxyecdysone dioxolane derivatives, a novel group of MDR modulator agents

The synthesis, structure elucidation and the complete (1)H and (13)C signal assignment of a series of dioxolane derivatives of 20-hydroxyecdysone, synthesized as novel modulators of multidrug resistance, are presented. The structures and NMR signal assignment were established by comprehensive one-dimensional and two-dimensional NMR spectroscopy supported by mass spectrometry.

Application of Two‐Dimensional NMR Spectroscopy to Metabotyping Laboratory Escherichia coli Strains

NMR Spectroscopy has been established as a major tool for identification and quantification of metabolites in a living system. Since the metabolomics era began, one-dimensional NMR spectroscopy has been intensively employed due to its simplicity and quickness. However, it has suffered from an inevitable overlap of signals, thus leading to inaccuracy in identification and quantification of metabolites. Two-dimensional (2D) NMR has emerged as a viable alternative because it can offer higher accuracy in a reasonable amount of time. We employed (1) H,(13) C-HSQC to profile metabolites of six different laboratory E. coli strains. We identified 18 metabolites and observed clustering of six strains according to their metabolites. We compared the metabolites among the strains, and found that a) the strains specialized for protein production were segregated; b) XL1-Blue separated itself from others by accumulating amino acids such as alanine, aspartate, glutamate, methionine, proline, and lysine; c) the strains specialized for cloning purpose were spread out from one another; and d) the strains originating from B strain were characterized by succinate accumulation. This work shows that 2D-NMR can be applied to identify a strain from metabolite analysis, offering a possible alternative to genetic analysis to identify E. coli strains.

NMR spectroscopic and MS/MS spectrometric characterization of a new lipopeptide antibiotic bacillopeptin B1 produced by a marine sediment-derived Bacillus amyloliquefaciens SH-B74

Bacillus species have the ability to secrete lipopeptide antibiotics under both in vivo and in vitro conditions.1, 2, 3, 4 Bacillus lipopeptides are versatile antibiotics composed mainly of three families—iturins, plipastatins (or fengcyins) and surfactins. Iturins and plipastatins are fungicides and have potential utilization in the biological control of fungal plant pathogens.5 Marine-derived microorganisms have arisen as a focus of research during recent decades, and numerous novel metabolites with excellent biological activity have been reported.6, 7 In the present work, compound 1 was isolated and purified from the fermentation broth of a marine sediment-derived B. amyloliquefaciens SH-B74. The structure of compound 1 was characterized by one-dimensional and two-dimensional NMR spectroscopy as well as tandem mass spectrometry (MS/MS) analysis. Finally, the antagonistic activities of compound 1 to several plant pathogens were also evaluated in vitro by the paper disc-agar diffusion assay.

Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery

In fragment-based drug discovery, the weak affinities exhibited by fragments pose significant challenges for screening. Biophysical techniques are used to address this challenge, but there is no clear consensus on which cascade of methods is best suited to identify fragment hits that ultimately translate into bound X-ray structures and provide bona fide starting points for synthesis. We have benchmarked an integrated biophysical approach for fragment screening and validation against Mycobacterium tuberculosis pantothenate synthetase. A primary screen of 1,250 fragments library was performed by thermal shift, followed by secondary screen using one-dimensional NMR spectroscopy (water ligand observed gradient spectroscopy and saturation transfer difference binding experiments) and ultimate hit validation by isothermal titration calorimetry and X-ray crystallography. Our multibiophysical approach identified three distinct binding sites for fragments and laid a solid foundation for successful structure-based elaboration into potent inhibitors.

Thermal Degradation and Kinetics of Alginate Polyurethane Hybrid Material Prepared from Alginic Acid as a Polyol

Alginate polyurethane hybrid materials are prepared by varying mole ratio of 2, 4-TDI as a di-isocyanate and alginic acid as a polyol in presence of dimethyl sulfoxide (DMSO) as a solvent. FT-IR and 13C one-dimensional (1D) solid state NMR (SSNMR) spectroscopy indicates that alginic acid is converted into alginate-polyurethane hybrid material via urethane linkage. Surface morphology of alginate-polyurethane hybrids changes by varying alginic acid: TDI ratio. The peak at near 221 °C in DSC thermogram of alginic acid (Alg) is shifted to higher temperature in alginate-polyurethane hybrid (Algpu1 and Algpu2). TGA study shows that alginate-polyurethane hybrid prepared using alginic acid: TDI = 1:1 (Algpu2) is more stable than alginic acid: TDI = 1:0.5 (Algpu1) at 300 °C. Kinetic analysis was performed to fit with TGA data, where the entire degradation process has been considered as three consecutive 1st order reactions. This study shows that thermal stability of alginate-polyurethane hybrid material was increased by adjusting mole ratio of 2, 4-TDI and alginic acid.

Phosphorescence Imaging of Living Cells with Amino Acid-Functionalized Tris(2-phenylpyridine)iridium(III) Complexes

A series of nine luminescent cyclometalated octahedral iridium(III) tris(2-phenylpyridine) complexes has been synthesized, functionalized with three different amino acids (glycine, alanine, and lysine), on one, two, or all three of the phenylpyridine ligands. All starting complexes and final compounds have been fully analyzed by one-dimensional (1D) and two-dimensional (2D) NMR spectroscopy, and photophysical data have been obtained for all the mono-, bis-, and tri- substituted iridium(III) complexes. Cellular uptake and localization have been studied with flow cytometry and confocal microscopy, respectively. Confocal experiments demonstrate that all nine substituted iridium(III) complexes show variable uptake in the tumor cells. The monosubstituted iridium(III) complexes give the highest cellular uptake, and the series substituted with lysines shows the highest toxicity. This systematic study of amino acid-functionalized Ir(ppy)(3) complexes provides guidelines for further functionalization and possible implementation of luminescent iridium complexes, for example, in (automated) peptide synthesis or biomarker specific targeting.

IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches.

BackgroundOne of the most promising aspects of metabolomics is metabolic modeling and simulation. Central to such applications is automated high-throughput identification and quantification of metabolites. NMR spectroscopy is a reproducible, nondestructive, and nonselective method that has served as the foundation of metabolomics studies. However, the automated high-throughput identification and quantification of metabolites in NMR spectroscopy is limited by severe spectral overlap. Although numerous software programs have been developed for resolving overlapping resonances, as well as for identifying and quantifying metabolites, most of these programs are frequency-domain methods, considerably influenced by phase shifts and baseline distortions, and effective only in small-scale studies. Almost all these programs require multiple spectra for each application, and do not automatically identify and quantify metabolites in batches.ResultsWe created IQMNMR, an R package that integrates a relaxation algorithm, digital filter, and similarity search algorithm. It differs from existing software in that it is a time-domain method; it uses not only frequency to resolve overlapping resonances but also relaxation time constants; it requires only one NMR spectrum per application; is uninfluenced by phase shifts and baseline distortions; and most important, yields a batch of quantified metabolites.ConclusionsIQMNMR provides a solution that can automatically identify and quantify metabolites by one-dimensional proton NMR spectroscopy. Its time-domain nature, stability against phase shifts and baseline distortions, requirement for only one NMR spectrum, and capability to output a batch of quantified metabolites are of considerable significance to metabolic modeling and simulation.IQMNMR is available at http://cran.r-project.org/web/packages/IQMNMR/.

Metabolomic Study on the Halophyte Suaeda salsa in the Yellow River Delta

Plant metabolomics has been well established and applied across multiple fields including medicine, biotechnology, and environmental sciences in the post-genomic era. The Chenopodiaceae C(3) halophyte Suaeda salsa is the most important plant species in the vegetation of saline soil and even intertidal zone in the Yellow River Delta, which is economically consumed as food, widely used as a bioindicator of environmental stresses (salinity, drought, and pollution) and typically applied for the phyto-remediation of degraded wetland. However, no global studies have been focused on the metabolic profile of this halophyte which is widely applied in environment related research areas. In metabolomics, the first crucial step is the preparation of plant samples. In this work, several strategies of metabolite extraction from this C(3) halophytes S. salsa were evaluated and the metabolic profile was characterized by NMRbased metabolomics. Multiple replicates of plant tissues (approx. 250 mg whole fresh weight of leaves and stems) were homogenized by a high throughput automated Precellys 24 bead-based homogenizer and then extracted using the following solvent systems of varying polarities:methanol, water, methanol/water, methanol/chloroform/water, and acetonitrile. The hydrophilic metabolites were analyzed using one-dimensional proton NMR spectroscopy, and the subsequent NMR spectra were evaluated by principal components analysis (PCA). Each extraction protocol revealed unique metabolic profile from S. salsa. Overall, the quality of each extraction protocol was assessed based on the yield, reproducibility, ease, and speed, and we concluded that the solvent of methanol/water was preferable for the metabolite extraction due to its highest reproducibility, ease, and speed, and considerably high yield. Validation of methanol/ water (1:1) solvent also showed a high degree of reproducibility with technical variation being considerably lower than biological variation in S. salsa samples. This demonstrated the quality and robustness of the methanol/water extraction method for NMRbased metabolomics studies.

An In Vitro Spectroscopic Analysis to Determine the Chemical Composition of the Precipitate Formed by Mixing Sodium Hypochlorite and Chlorhexidine

Introduction The purpose of this in vitro study was to determine the chemical composition of the precipitate formed by mixing sodium hypochlorite (NaOCl) and chlorhexidine (CHX) and the relative molecular weight of the components. Methods Using commercially available CHX gluconate, a 2% solution was formed and mixed in a 1:1 ratio with commercially available NaOCl producing a brown precipitate. The precipitate as well as a mixture of precipitate and pure CHX diacetate was then analyzed using one-dimensional and two-dimensional NMR spectroscopy. Results The one-dimensional and two-dimensional NMR spectra were fully assigned in terms of chemical shifts of all proton and carbon atoms in intact CHX. This permitted identification of two major CHX breakdown products, neither of which are parachloroaniline (PCA). Both products are related to PCA in that they are parasubstituted benzene compounds. Based on NMR data and a proposed mechanism of CHX breakdown, the products appear to be parachlorophenylurea (PCU) and parachlorophenylguanidyl-1,6-diguanidyl-hexane (PCGH). Conclusions Based on this in vitro study, the precipitate formed by NaOCl and CHX is composed of at least two separate molecules, all of which are smaller in size than CHX. Along with native CHX, the precipitate contains two chemical fragments derived from CHX (PCU and PCGH), neither of which are PCA.

Glaucasides A–C, three saikosaponins from Atriplex glauca L. var. ifiniensis (Caball) Maire

From the roots of Atriplex glauca L. var. ifiniensis (Caball) Maire (syn. of Atriplex parvifolia Lowe var. genuina Maire), three new saikosaponins designated as glaucasides A-C (1-3) were isolated together with the known 3-O-β-D-glucopyranosyl-(1 → 2)-β-D-galactopyranosyl-saikogenin F (4). The structures of the new compounds were elucidated by extensive analysis of one-dimensional and two-dimensional NMR spectroscopy, FABMS, HR-ESIMS and chemical evidence as 13β,28-epoxy-16β,21β-dihydroxyolean-11-en-3β-yl O-β-D-[2-O-sulfate]-glucopyranosyl-(1 → 2)-α-L-arabinopyranoside (1), 13β,28-epoxy-16β,21β-dihydroxyolean-11-en-3β-yl O-β-D-[2-O-sulfate]-glucopyranosyl-(1 → 2)-α-L-arabinopyranosyl 21-O-{4-(secbutylamido)-butanoyl ester} (2) and 3-O-β-D-glucopyranosyl-(1 → 2)-β-D-galactopyranosyl saikogenin G (3). The cytotoxic activities of these compounds were evaluated against the HT-29 and HCT 116 human colon cancer cell lines.

Aroma WaterLOGSY: a fast and sensitive screening tool for drug discovery

One-dimensional NMR spectroscopy has proven to be a powerful technique for screening compound libraries in drug discovery. We report a novel water ligand-observed gradient spectroscopy (WaterLOGSY) pulse sequence, named Aroma WaterLOGSY, that selectively detects aromatic WaterLOGSY signals from compounds or ligands. In the Aroma WaterLOGSY, water magnetization is untouched after water excitation and utilizes the whole period of the remaining pulse sequence to relax back to the +z direction. Due to the phase cycling design, the water magnetization is allowed to relax for the period of two full scans before it gets inverted again. Therefore, the recycle delay can be significantly shortened. Within similar experimental time, Aroma WaterLOGSY shows approximately two times higher sensitivity than the standard scheme. This method also allows the use of non-deuterated reagents, thereby accelerating experimental set-up time for ligand-binding studies.

Purification and NMR studies on Phosphatase domain of UBLCP1

【UBLCP1 is composed of Ubiquitin Like domain and RNA Polymerase II Phosphatase I domain. Phosphatase domain (25.9KDa) has been cloned into the E.coli using pET32a vector with TEV protease cleavage site and successfully purified as a monomer using affinity chromatography and histidine tag was cleaved with TEV protease for structural studies. Our results indicated that the Phosphatase domain showed well-defined folded structure based on data from one-dimensional and two-dimensional NMR spectroscopy. Data form circular dichroism also suggested that Phosphatase domain consisted of both ${\alpha}$ -helix and ${\beta}$ -sheet. This information will be used for detailed structural study of UBLCP1.】

Phosphorylation of Plant Translation Initiation Factors by CK2 Enhances the in Vitro Interaction of Multifactor Complex Components

CK2 phosphorylates a wide variety of substrates, including translation initiation factors. A mass spectrometric approach was used to identify residues phosphorylated by CK2, which may regulate the activity of initiation factors during the translation initiation process in plants. CK2 in vitro phosphorylation sites were identified in wheat and Arabidopsis thaliana eIF2alpha, eIF2beta, eIF5, and wheat eIF3c. Native wheat eIF5 and eIF2alpha were found to have phosphorylation sites that corresponded to some of the in vitro CK2 phosphorylation sites. A large number of the CK2 sites identified in this study are in conserved binding domains that have been implicated in the yeast multifactor complex (eIF1-eIF3-eIF5-eIF2-GTP-Met-tRNA(i)(Met)). This is the first study to demonstrate that plant initiation factors are capable of forming a multifactor complex in vitro. In addition, the interaction of factors within these complexes was enhanced both in vitro and in native extracts by phosphorylation of one or more initiation factors by CK2. The importance of CK2 phosphorylation of eIF5 was evaluated by site-directed mutagenesis of eIF5 to remove CK2 phosphorylation sites. Removal of CK2 phosphorylation sites from eIF5 inhibits the CK2-mediated increase in eIF5 interaction with eIF1 and eIF3c in pulldown assays and reduces the eIF5-mediated stimulation of translation initiation in vitro. These results suggest a functional role for CK2 phosphorylation in the initiation of plant translation.

Synthesis and photochemistry of two quinoline analogs of the perimidinespirohexadienone family of photochromes

We report the detailed synthesis and photochemistry of two analogs (specifically 3,5-di- tert-butyl-7′-methyl- and 3,5-di- tert-butyl-7′,9′-dimethyl-1′,3′-dihydrospirocyclohexa[2,5]diene-1,2′-pyrido[4,3,2-de]quinazolin-4-one) of the perimidinespirohexadienone (3,5-di- tert-butyl-1′,3′-dihydrospirocyclohexa[2,5]diene-1,2′-perimidin-4-one) family of photochromes in which the naphthalene moiety of the parent is replaced by a quinoline, and compare them to the parent compound. Molar absorptivities of both the short wavelength spirocyclic isomer (SW) and long wavelength quinonimine isomer (LW) of each were determined by a combination of proton NMR and UV–vis spectroscopy in solvents of varying polarity. Quantum yield measurements for photoisomerization of SW to LW are reported in those same solvents, with qualitative extrapolation to additional solvents. The position and rate of the thermal equilibrium reverting LW to SW is estimated for these compounds. The 9′-methyl in SW (6-methyl in LW) is found to be essential for complete reversion of LW to SW in the dark. Finally one-dimensional NOE NMR spectroscopy was used to conclusively determine the structure of LW for the quinoline analogs as the 4-(5-aminoquinolin-4-ylimino)-2,6-di- tert-butylcyclohexa-2,5-dienone resulting from opening toward the quinoline nitrogen, rather than the 4-(4-aminoquinolin-5-ylimino) structure that would result from spirocyclic ring opening away from the quinoline nitrogen which had been initially proposed by Minkin et al. for very similar compounds [V.I. Minkin, V.N. Komissarov, V.A. Kharlanov, Perimidinespirocyclohexadienones, in: J.C. Crano, R.J. Guglielmetti (Eds.), Organic Photochromic and Thermochromic Compounds, vol. 1, Plenum Press, New York, 1999, pp. 315–340, and references therein].

19F NMR Spectroscopy for the Analysis of RNA Secondary Structure Populations

Labeling of RNA with site-specific fluorine atoms has become straightforward in recent years and in particular has become an integrated part of engineered functional RNA with therapeutic potential, e.g. for siRNA technologies. Here, we demonstrate that temperature-dependent one-dimensional (19)F NMR spectroscopy of oligoribonucleotides is a powerful tool to obtain direct information on the conformational behavior. The approach is particularly useful for the quantification of monomolecular vs bimolecular secondary structure equilibria.

DYNAMICS OF IMINE AND ACETOPHENONE DERIVATIVES IN SOLUTION STUDIED BY ONE-DIMENSIONAL DIFFUSION-ORDERED NMR SPECTROSCOPY (DOSY)

This paper describes the usefulness of one-dimensional diffusion-ordered NMR spectroscopy (1D-DOSY) in investigating dynamics and interactions of molecules in solution as well as in analyzing the structure of molecules. We synthesized the three imines, N-benzylidene-4-methylbenzene-Sulfonamide (1), N-(4-chloro-benzylidene)4-methyl-benzene-sulfonamide (2), and N- (4-methoxybenzylidene)-4-methyl-benzene sulfonamide (3), and acetophenone (4) and its three derivatives, 4-chloroacetophenone (5), 4-nitro-acetophenone (6), and 4-methoxyaceto -phenone (7). 1D-DOSY was applied to a mixture of compounds (1), (2), and (3) and to a mixture of compounds (4), (5), (6), and (7). Although 1 H NMR chemical shifts of the molecules in the mixtures resembled one another in the surrounding, we could distinguish signals of the individual molecules in each mixture on the basis of the NMR data and the values of the diffusion coefficient. Also, we could found the correlation of the measured diffusion coefficients and the calculated molecular volumes.

C−H Bond Activation of Coordinated Pyridine: Ortho-Pyridyl-Ditechnetiumhydridocarbonyl Metal Cyclus. Crystal Structure and Dynamic Behavior in Solution

The reaction of pyridine with ditechnetium decacarbonyl [Tc2(CO)10] (1) leads to a novel ortho-pyridyl-ditechnetium hydrido complex, [Tc2(mu-H)(mu-NC5H4)(NC5H5)2(CO)6] (2) and its precursor [Tc2(mu-CO)2(NC5H5)2(CO)6] (3). At ambient temperature 1 was found to react slowly with pyridine to afford the substitution product 3 after 120 h. However, heating the reaction mixture to reflux exclusively leads to the pyridine-ortho-metalated complex 2 in only 30 min. Similarly, complex 3 can be converted completely into 2 upon heating in pyridine for 30 min. Both compounds 2 and 3 were characterized by NMR spectroscopy and X-ray analysis. Both compounds 2 and 3 show a complex dynamic behavior in solution that was investigated by one-dimensional and two-dimensional NMR spectroscopy. Both compounds 2 and 3 show isomerization in solution according to the relative position of the non-bridging pyridine ligands. For 2 the existence of three isomers was shown at equilibrium conditions, 2a (56%) with trans-diaxial, 2b (38%) with cis-diaxial, and 2c (6%) with axial-equatorial arrangement of the non-bridging pyridines. For 3 an equilibrium was detected between two isomers, 3a (67%) with a cis-diaxial and 3b (33%) with a trans-diaxial arrangement of the pyridines.

The Factor H Variant Associated with Age-related Macular Degeneration (His-384) and the Non-disease-associated Form Bind Differentially to C-reactive Protein, Fibromodulin, DNA, and Necrotic Cells

Recently, a polymorphism in the complement regulator factor H (FH) gene has been associated with age-related macular degeneration. When histidine instead of tyrosine is present at position 384 in the seventh complement control protein (CCP) domain of FH, the risk for age-related macular degeneration is increased. It was recently shown that these allotypic variants of FH, in the context of a recombinant construct corresponding to CCPs 6-8, recognize polyanionic structures differently, which may lead to altered regulation of the alternative pathway of complement. We show now that His-384, corresponding to the risk allele, binds C-reactive protein (CRP) poorly compared with the Tyr-384 form. We also found that C1q and phosphorylcholine do not compete with FH for binding to C-reactive protein. The interaction with extracellular matrix protein fibromodulin, which we now show to be mediated, at least in part, by CCP6-8 of FH, occurs via the polypeptide of fibromodulin and not through its glycosaminoglycan modifications. The Tyr-384 variant of FH bound fibromodulin better than the His-384 form. Furthermore, we find that CCP6-8 is able to interact with DNA and necrotic cells, but in contrast the His-384 allotype binds these ligands more strongly than the Tyr-384 variant. The variations in binding affinity of the two alleles indicate that complement activation and local inflammation in response to different targets will differ between His/His and Tyr/Tyr homozygotes.