Two-dimensional NMR Spectroscopy Research Articles

NMR-based conformational analysis of 2′,6-disubstituted uridines and antiviral evaluation of new phosphoramidate prodrugs

Six novel phosphoramidate prodrugs of uridine analogues, with structural modifications introduced at the 6- and 2′,6-positions, have been prepared and evaluated for selective antiviral activity against hepatitis C virus, as well as other positive-stranded RNA viruses. An analysis of the conformational properties of the parent nucleosides was carried out using two-dimensional NMR spectroscopy based experiments, highlighting a 3′-endo (North) sugar puckering preference and syn orientation.

Natural Abundance (17)O DNP Two-Dimensional and Surface-Enhanced NMR Spectroscopy.

Due to its extremely low natural abundance and quadrupolar nature, the (17)O nuclide is very rarely used for spectroscopic investigation of solids by NMR without isotope enrichment. Additionally, the applicability of dynamic nuclear polarization (DNP), which leads to sensitivity enhancements of 2 orders of magnitude, to (17)O is wrought with challenges due to the lack of spin diffusion and low polarization transfer efficiency from (1)H. Here, we demonstrate new DNP-based measurements that extend (17)O solid-state NMR beyond its current capabilities. The use of the PRESTO technique instead of conventional (1)H-(17)O cross-polarization greatly improves the sensitivity and enables the facile measurement of undistorted line shapes and two-dimensional (1)H-(17)O HETCOR NMR spectra as well as accurate internuclear distance measurements at natural abundance. This was applied for distinguishing hydrogen-bonded and lone (17)O sites on the surface of silica gel; the one-dimensional spectrum of which could not be used to extract such detail. Lastly, this greatly enhanced sensitivity has enabled, for the first time, the detection of surface hydroxyl sites on mesoporous silica at natural abundance, thereby extending the concept of DNP surface-enhanced NMR spectroscopy to the (17)O nuclide.

Microwave-assisted synthesis of cyclodextrin polyurethanes

Cyclodextrin (CD) has often been incorporated into polyurethanes in order to facilitate its use in encapsulation or removal of organic species for various applications. In this work a microwave-assisted method has been developed to produce polyurethanes consisting of α-, β-, and γ-CD and three common diisocyanates. As compared to conventional heating, this new synthetic method saves energy, significantly reduces reaction time, and gets similar or improved yield. The reaction products have been fully characterized with (13)C, (1)H, and two-dimensional NMR spectroscopy. With suitable stoichiometry of starting CD and diisocyanate, the resulting CD polyurethane is organic-soluble and water-insoluble and is shown to remove Nile red dye and phenol from water. Possible applications include the removal of undesirable materials from process streams, toxic compounds from the environment, and encapsulation of color or fragrance molecules.

Novel synthesis, structural analysis, photophysical properties and theoretical study of 2,4,5-tris(2-pyridyl)imidazole

2,4,5-Tris(2-pyridyl)imidazole has been successfully synthetized by a novel synthetic route and fully characterized by FT-IR,UV–Vis and fluorescence spectroscopy, one- and two-dimensional NMR spectroscopy (1H, 13C{1H} ATP, 1H–1H COSY, NOESY 1H–13C HSQC and HMBC) high-resolution, mass spectrometry (HR-FAB+), and single-crystal X-ray diffraction analysis. Additionally, the molecular geometry, vibrational frequencies and infrared intensities were calculated by density functional theory using the M06/6-31G(d) level of theory, showing good agreement with the experimental results. The title compound showed interesting photophysical properties, which were studied experimentally in solution and in the solid state by UV–Vis and fluorescence spectroscopy, and theoretically using TD-DFT calculations. Natural and Mulliken atomic charges and the molecular electrostatic potential (MEP) have been mapped.

Structure of the O-specific polysaccharide from the deep-sea marine bacterium Idiomarina abyssalis КММ 227T containing a 2-O-sulfate-3-N-(4-hydroxybutanoyl)-3,6-dideoxy-d-glucose

The O-specific polysaccharide was isolated from the lipopolysaccharide of type strain Idiomarina abyssalis КММ 227T and studied by sugar analysis, Smith degradation, and two-dimensional 1H and 13C NMR spectroscopy including 1H,1H-TOCSY, 1H,1H-COSY, 1H,1H-ROESY, 1H,13C-HSQC, 1H,13C-HMBC, 1H,13C-H2BC and 1H,13C-HSQC-TOCSY experiments. The new structure of the O-specific polysaccharide of I. abyssalis КММ 227T containing 2-O-sulfate-3-N-(4-hydroxybutanoyl)-3,6-dideoxy-d-glucose was established: [Display omitted]

Probing Metabolite Space of Escherichia coli via Growth Medium Composition as Monitored by Two-Dimensional NMR Spectroscopy.

As for recombinant protein production, Escherichia coli is one of the most frequently employed hosts because it offers a simple and inexpensive, but rapid and high-yield system in addition to the vast information on its molecular genetics and biology. However, due to its prokaryotic nature, it often fails to produce eukaryotic proteins in a desired form. To devise a systematic way leading to a condition that produces a large amount of usable proteins, we attempted to monitor intracellular metabolites under various conditions, and to link them to recombinant protein production. With such an intention, we identified 31 metabolites from cells grown in different media by using two-dimensional (2D) NMR spectroscopy. Our results revealed that 1) the level of betaine was low, while that of glutamic acid was high when grown in minimal media; 2) the level of glycerol was constantly high in all cases; 3) the level of oxidized glutathione was lower in Luria broth (LB); and 4) the level of leucine was low in minimal media. We hope this work might shed light onto how to improve production of the target proteins by metabolite profiling.

Single-beam spectrally controlled two-dimensional Raman spectroscopy

Vibrational modes are often localized in certain regions of a molecule, and so the coupling between these modes is sensitive to the molecular structure. Two-dimensional vibrational spectroscopy can probe the strength of this coupling in a manner analogous to two-dimensional NMR spectroscopy, but on ultrafast timescales. Here, we demonstrate how two-dimensional Raman spectroscopy, based on fifth-order optical nonlinearity, can be performed with a single beam of shaped femtosecond optical pulses. Our spectroscopy scheme offers not only a major simplification of the conventional set-up, but also an inherent elimination of a competing nonlinear signal, which overwhelms the desired signal in other schemes and carries no coupling information. 2D Raman spectroscopy, based on fifth-order optical nonlinearity, is performed with a single beam of shaped fs optical pulses. The scheme inherently eliminates the cascade signal, making the vibrational coupling information easy to extract.

Structures and Biosynthesis of Corvol Ethers--Sesquiterpenes from the Actinomycete Kitasatospora setae.

Here we present the functional characterization of a sesquiterpene cyclase from Kitasatospora setae. The enzyme converts the sesquiterpene precursor farnesyl diphosphate (FPP) into two previously unknown and unstable sesquiterpene ethers for which we propose the trivial names corvol ethers A and B. Both compounds were purified and their structures were determined by one- and two-dimensional NMR spectroscopy. A biosynthetic mechanism for the FPP cyclization by the corvol ether synthase was proposed. The results from the incubation experiments of the corvol ether synthase with isotopically labeled precursors were in line with this mechanism, while alternative mechanisms could clearly be ruled out.

An extended CCR5 ECL2 peptide forms a helix that binds HIV-1 gp120 through non-specific hydrophobic interactions.

C-C chemokine receptor 5 (CCR5) serves as a co-receptor for HIV-1. The CCR5 N-terminal segment, the second extracellular loop (ECL2) and the transmembrane helices have been implicated in binding the envelope glycoprotein gp120. Peptides corresponding to the sequence of the putative ECL2 as well as peptides containing extracellular loops 1 and 3 (ECL1 and ECL3) were found to inhibit HIV-1 infection. The aromatic residues in the C-terminal half of an ECL2 peptide were shown to interact with gp120. In the present study, we found that, in aqueous buffer, the segment Q188-Q194 in an elongated ECL2 peptide (R168-K197) forms an amphiphilic helix, which corresponds to the beginning of the fifth transmembrane helix in the crystal structure of CCR5. Two-dimensional saturation transfer difference NMR spectroscopy and dynamic filtering studies revealed involvement of Y187, F189, W190 and F193 of the helical segment in the interaction with gp120. The crystal structure of CCR5 shows that the aromatic side chains of F189, W190 and F193 point away from the binding pocket and interact with the membrane or with an adjacent CCR5 molecule, and therefore could not interact with gp120 in the intact CCR5 receptor. We conclude that these three aromatic residues of ECL2 peptides interact with gp120 through hydrophobic interactions that are not representative of the interactions of the intact CCR5 receptor. The HIV-1 inhibition by ECL2 peptides, as well as by ECL1 and ECL3 peptides and peptides corresponding to ECL2 of CXCR4, which serves as an alternative HIV-1 co-receptor, suggests that there is a hydrophobic surface in the envelope spike that could be a target for HIV-1 entry inhibitors. The structures and NMR data of ECL2S (Q186-T195) were deposited under Protein Data Bank ID 2mzx and BioMagResBank ID 25505.

Structural studies of conformers of 3-(N-acetyl-N-arylamino)tropones by heteronuclear, two-dimensional, and dynamic NMR spectroscopy and X-ray diffraction analysis

Acylation of 5,7-di(tert-butyl)-2-(5,8-dimethyl-4-piperidinoquinolin-2-yl)-3-(3,5-dimethylphenylamino)tropone leads to the corresponding 3-(N-acetyl-N-arylamino)tropone. Heteronuclear, two-dimensional, and dynamic NMR spectroscopy were used to determine structures of conformers of N-acetyl-3-arylaminotropone. The structure of 3-[N-acetyl-N(3,5-dimethylphenyl)amino]-5,7-di(tert-butyl)-2-(5,8-dimethyl-4-piperidinoquinolin-2-yl)tropone was established by X-ray diffraction studies.

Application of selective two-dimensional exchange NMR spectroscopy to the study of molecular dynamic processes

A vector model of the multiplet-selective excitation of spin systems by a three-pulse sequence is considered, and, on this basis, a new two-dimensional exchange NMR spectroscopy technique is suggested. This technique provides means to investigate intramolecular and intermolecular chemical and spin exchanges by observing the dynamic behavior of the multiplet pattern of a nucleus that is scalarwise coupled with the unobservable nucleus undergoing exchange.

Stable lanthanum(III) and neodymium(III) sandwich-type complexes based on porphyrazine with annulated diazepine rings

Starting from tetrakis(5,7-bis(4-tert-butylphenyl)-6H-1,4-diazepino)[2,3-b,g,l,q]porphyrazine and the corresponding lanthanide(III) salts, novel homoleptic double-decker sandwich-type complexes with early rare earth metals (La and Nd) were prepared. The compounds obtained were characterized by a combination of high resolution MALDI TOF/TOF mass spectrometry, Uv–Vis/NIR and two-dimensional NMR spectroscopy (COSY and NOESY). For the first time the electrochemical behavior of the double-decker complex based on tetradiazepinoporphyrazine ligand was studied by cyclic voltammetry and square-wave voltammetry. Despite the large radius of the lanthanide(III) ion, the resulting compounds showed high stability towards dissociation both in the solid state and in solution, which arose from specific interligand interactions provided by the diazepine heterocyclic moieties.

Structural characterization and in vivo evaluation of β-Hairpin peptidomimetics as specific CXCR4 imaging agents.

The CXCR4 chemokine receptor is integral to several biological functions and plays a pivotal role in the pathophysiology of many diseases. As such, CXCR4 is an enticing target for the development of imaging and therapeutic agents. Here we report the evaluation of the POL3026 peptidomimetic template for the development of imaging agents that target CXCR4. Structural and conformational analyses of POL3026 and two of its conjugates, DOTA (POL-D) and PEG12-DOTA (POL-PD), by circular dichroism, two-dimensional NMR spectroscopy and molecular dynamics calculations are reported. In silico observations were experimentally verified with in vitro affinity assays and rationalized using crystal structure-based molecular modeling studies. [(111)In]-labeled DOTA conjugates were assessed in vivo for target specificity in CXCR4 expressing subcutaneous U87 tumors (U87-stb-CXCR4) through single photon emission computed tomography (SPECT/CT) imaging and biodistribution studies. In silico and in vitro studies show that POL3026 and its conjugates demonstrate similar interactions with different micelles that mimic cellular membrane and that the ε-NH2 of lysine(7) is critical to maintain high affinity to CXCR4. Modification of this group with DOTA or PEG12-DOTA led to the decrease of IC50 value from 0.087 nM for POL3026 to 0.47 nM and 1.42 nM for POL-D and POL-PD, respectively. In spite of the decreased affinity toward CXCR4, [(111)In]POL-D and [(111)In]POL-PD demonstrated high and significant uptake in U87-stb-CXCR4 tumors compared to the control U87 tumors at 90 min and 24 h post injection. Uptake in U87-stb-CXCR4 tumors could be blocked by unlabeled POL3026, indicating specificity of the agents in vivo. These results suggest POL3026 as a promising template to develop new imaging agents that target CXCR4.

Neutral Pectin side chains of Amaranth (Amaranthus hypochondriacus) contain long, partially branched Arabinans and short galactans, both with terminal arabinopyranoses.

Amaranth is a pseudocereal of high nutritional value, including a high dietary fiber content. Amaranth dietary fiber was suggested to contain large amounts of neutral rhamnogalacturonan I side chains. In this study, endo-arabinanase and endo-galactanase were used to liberate arabinan and galactan oligosaccharides from amaranth fiber. The liberated oligosaccharides were identified by high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and HPLC-MS(n) using standard compounds, which were isolated from amaranth, sugar beet, potato, and red clover sprouts and characterized by one- and two-dimensional NMR spectroscopy. It was demonstrated that insoluble amaranth arabinans have linear and branched areas, with the O-3 position being the dominant branching point. Minor amounts of branches at position O-2 and double substitution were also found. Amaranth arabinans were also demonstrated to contain terminal α-(1→5)-linked l-arabinopyranose units. In addition, it was evidenced that galactans from amaranth seeds are composed of β-(1→4)-linked d-galactopyranose units, which can also be terminated with l-arabinopyranose units. In direct comparison to structural elucidation of amaranth fiber by using methylation analysis, the advantage of the enzymatic approach over methylation analysis was demonstrated.

A unique capsular polysaccharide structure from the psychrophilic marine bacterium Colwellia psychrerythraea 34H that mimics antifreeze (glyco)proteins.

The low temperatures of polar regions and high-altitude environments, especially icy habitats, present challenges for many microorganisms. Their ability to live under subfreezing conditions implies the production of compounds conferring cryotolerance. Colwellia psychrerythraea 34H, a γ-proteobacterium isolated from subzero Arctic marine sediments, provides a model for the study of life in cold environments. We report here the identification and detailed molecular primary and secondary structures of capsular polysaccharide from C. psychrerythraea 34H cells. The polymer was isolated in the water layer when cells were extracted by phenol/water and characterized by one- and two-dimensional NMR spectroscopy together with chemical analysis. Molecular mechanics and dynamics calculations were also performed. The polysaccharide consists of a tetrasaccharidic repeating unit containing two amino sugars and two uronic acids bearing threonine as substituent. The structural features of this unique polysaccharide resemble those present in antifreeze proteins and glycoproteins. These results suggest a possible correlation between the capsule structure and the ability of C. psychrerythraea to colonize subfreezing marine environments.

One-pot synthesis of water-soluble, β-cyclodextrin-based polyrotaxanes in a homogeneous water system and its use in bio-applications.

A small, nano-sized, water-soluble polyrotaxane (PR) was synthesized using a highly efficient one-pot synthesis strategy in a homogeneous water system, formed from β-cyclodextrin-(COOH)2, poly(propylene glycol)bis(2-aminopropyl ether) (PPG, 2 kDa) and a mono-(6-azido-6-desoxy)-β-cyclodextrin stopper via room temperature click chemistry. β-cyclodextrin-(COOH)2 and PR were characterized by one- and two-dimensional NMR as well as by high resolution transmission electron microscopy (HR-TEM). The number of carboxyl groups in one PR was determined by 1H NMR. Two-dimensional diffusion-ordered NMR spectroscopy (2D DOSY) and nuclear Overhauser enhancement spectroscopy (2D NOESY) show that β-cyclodextrin-(COOH)2 and PPG successfully formed an inclusion complex. HR-TEM revealed the morphology of water-soluble PR as a spherical nanoparticle with a size of approximately 3.5 nm ± 1.5 nm. PR was labeled with rhodamine to assess its biocompatibility and cell membrane penetrability in vitro. The in vivo real-time fluorescent imaging biodistribution experiments indicated that water-soluble PR can actively target tumor sites using an enhanced permeability and retention (EPR) effect, with a significantly prolonged blood circulation time in tumor-bearing mice.

Six new polyhydroxy steroidal glycosides from Dregea sinensis Hemsl

Absract The phytochemical investigation of the roots of Dregea sinensis Hemsl yielded six new polyhydroxy steroidal glycosides (1–6). The chemical structures have been elucidated on the basis of extensive one- and two-dimensional NMR spectroscopy, as well as by mass spectrometry. The cytotoxic activity of these compounds were evaluated in vitro while compounds 3 and 4 showed weak activity against human leukemia cells (HL-60) with IC 50 values of 14.10 μM and 19.16 μM, respectively.

Pretrichodermamide C and N-methylpretrichodermamide B, two new cytotoxic epidithiodiketopiperazines from hyper saline lake derived Penicillium sp.

Two new epidithiodiketopiperazines, pretrichodermamide C (1) and N-methylpretrichodermamide B (2) were isolated from the fungus Penicillium sp., derived from the sediment of a hyper saline lake located at Wadi El-Natrun in Egypt. The structures of 1 and 2 were unambiguously determined on the basis of one- and two-dimensional NMR spectroscopy and by high-resolution mass spectrometry, as well as by comparison with the literature. Compound 2 showed pronounced cytotoxicity against the murine lymphoma L5178Y cell line with an IC50 value of 2μM.

High-performance countercurrent chromatography separation of Peucedanum cervaria fruit extract for the isolation of rare coumarin derivatives.

For the first time, rare major and minor compounds from fruits of Peucedanum cervaria were isolated. High-performance countercurrent chromatography with two different solvent systems, heptane/ethyl acetate/methanol/water (3:2:3:2 and 2:1:2:1, v/v), was successfully used in the reversed-phase mode. A scale-up process from analytical to semipreparative in a very short time was developed. The structures of isolated compounds were evaluated by high-performance liquid chromatography with diode array detection and electrospray ionization mass spectrometry, gas chromatography with mass spectrometry, and one- and two-dimensional NMR spectroscopy. (8S,9R)-9-(3-Methylbutenoyloxy)-O-acetyl-8,9-dihydrooroselol (compound B), (8S,9R)-9-(2-methyl-Z-butenoyloxy)-O-acetyl-8,9-dihydrooroselol (edultin, compound C), and (8S,9R)-9-acetoxy-O-(2α-methylbutyryl)-8,9-dihydrooroselol (compound D) were obtained using heptane/ethyl acetate/methanol/water (2:1:2:1, v/v) in <40 min. The method yielded 4.6 mg of a mixture of compounds B and C (11:89) and 3.7 mg of compound D. These amounts were obtained from the crude extract (0.5 g) in a single run. Although the compounds are known, their isolation by countercurrent chromatography and the analysis of their relative stereochemistry by two-dimensional NMR spectroscopy have been performed for the first time. Additionally, heptane/ethyl acetate/methanol/water (3:2:3:2, v/v) led to the isolation of oxypeucedanin (1.2 mg; compound A). This is the first time that angular dihydrofuranocoumarin was isolated from plant extract by countercurrent chromatography.

Sulfono-γ-AApeptides as a new class of nonnatural helical foldamer.

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-γ-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-γ-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-γ-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports well- defined helical conformation of sulfono-γ-AApeptides in solution containing as few as five building blocks. Future development of sulfono-γ-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.