2D NOE Research Articles

Keeping PASE with WEFT: SHWEFT–PASE pulse sequences for 1H NMR spectra of highly paramagnetic molecules

Metalloproteins are a category of biomolecules in which the metal site is usually the locus of activity or function. In many cases, the metal ions are paramagnetic or have accessible paramagnetic states, many of which can be studied using NMR spectroscopy. Extracting useful information from (1)H NMR spectra of highly paramagnetic proteins can be difficult because the paramagnetism leads to large resonance shifts (~400 ppm), extremely broad lines, extreme baseline nonlinearity, and peak shape distortion. It is demonstrated that employing polychromatic and adiabatic shaped pulses in simple pulse sequences, then combining existing sequences, leads to significant spectral improvement for highly paramagnetic proteins. These sequences employ existing technology, with available hardware, and are of short duration to accommodate short nuclear T1 and T2. They are shown to display uniform excitation over large spectral widths (~75 kHz), accommodate high repetition rates, produce flat baselines over 75 kHz while maintaining peak shape fidelity, and can be used to reduce spectral dynamic range. High-spin (S = 5/2) metmyoglobin, a prototypical highly paramagnetic protein, was used as the test molecule. The resulting one-dimensional (1D) pulse sequences combine shaped pulses with super-water elimination Fourier transform, which can be further combined with paramagnetic spectroscopy to give shaped pulses with super-water elimination Fourier transform-paramagnetic spectroscopy. These sequences require, at most, direct current offset correction and minimal phasing. The performance of these sequences in simple (1)H 1D, 1D NOE, and two-dimensional NOESY experiments is demonstrated for metmyoglobin and Paracoccus denitrificans Co(2+)-amicyanin (S = 3/2), and employed to make new heme hyperfine resonance assignments for high-spin metBjFixLH(151-256), the heme sensing domain of Bradyrhizobium japonicum FixL.

Spatial structure of felodipine dissolved in DMSO by 1D NOE and 2D NOESY NMR spectroscopy

Small organic molecules in dissolved state exist as an ensemble of conformers. In this work conformation of felodipine in dimethyl sulphoxide was studied and dominant stable conformers were determined. Effective interatomic distances were obtained by means of NOE spectroscopy. Fractions of different conformers were estimated by comparing effective distances and those obtained from quantum-chemical calculation [8]; averaging of distances was made following the N-site jump model.

Synthesis of novel isoxazolidine analogues of homonucleosides

A general method for the synthesis of nucleobase-derived nitrones 4a–e by treatment of N-(2-oxoethyl)nucleobases with N-methylhydroxylamine is reported. The nitrones 4a–e were applied in the synthesis of isoxazolidine homonucleosides. Moderate diastereoselectivities (de 28–82%) were observed for cycloadditions between nitrones 4a–e and allyl alcohol with cis-isoxazolidines predominating. The stereochemistry of the substituted isoxazolidines was established based on an analysis of 2D NOE experiments for uracil-containing cycloadducts 6a and 7a. Cycloadditions of uracil-based nitrone 4a with vinyl-, allyl-, vinyloxymethyl- and allyloxymethylphosphonates gave the respective phosphonylated cis-isoxazolidines as the major adducts.

Synthesis of aryl-substituted or aryl-fused N-hydroxyethyl and N-hydroxymethypyrazole derivatives as potential ligands for the estrogen receptor

A new series of N-hydroxyethylpyrazole (12a–f) and N-hydroxymethylpyrazole derivatives (15a–f) were designed for their estrogenic activities, having a 11.0 ± 0.5 A distance between their two hydroxyl groups, aliphatic–OH and phenolic–OH similar to 17β-estradiol (E2) as an endogenous hormone. To synthesize the title compounds, the key intermediate 1,3-dicarbonyl derivatives (2 and 8), were treated with hydrazine hydrate to produce the pyrazole ring 5 and 9. Further hydroxyalkylation of the latter produced the title pyrazoles. The position of hydroxyethyl or hydroxymethyl substituents in the products was determined through 2D NOE NMR spectroscopy.

Synthesis of ru(bpy)3-viologen and its complex included by p-sulfonatocalix[4]arene in a U-type binding manner

Abstract A novel Ru(bpy)3–viologen guest RPV and a reference compound PV are well designed and synthesized. Ru(bpy)3 based guest compound RPV prefers to form a novel U-type complex RPV⊂SC4 with p-sulfonatocalix[4]arene (SC4) host. Binding manner of the complex has been fully studied by 1H NMR, ESI-MS and 2D NOE NMR spectra. The 1:1 Binding ratio is confirmed by UV–Vis measurement and the association constant is determined by 1H NMR titration. In this host–guest system, both Ru(bpy)3 and viologen group show strong interactions with the host SC4. Due to the unique U-type structure of RPV⊂SC4, the competitive interactions between Ru(bpy)3 and viologen group were investigated as well.

Cichorins B and C: two new benzo-isochromenes from Cichorium intybus

Two new benzo-isochromenes, named cichorins B (1) and C (2), were isolated from Cichorium intybus. The structures of the new compounds were elucidated by detailed spectroscopic analysis such as 1H, 13C NMR, COSY, HMQC, HMBC, and HR-EI-MS. Relative configurations of asymmetric centers of cichorins B and C were determined by the analysis of the 1H NMR coupling constants together with the 2D NOESY and 1D NOE experiments as well as from value.

Bioactive Hydroanthraquinones and Anthraquinone Dimers from a Soft Coral-Derived Alternaria sp. Fungus

Five new hydroanthraquinone derivatives, tetrahydroaltersolanols C-F (1-4) and dihydroaltersolanol A (5), and five new alterporriol-type anthranoid dimers, alterporriols N-R (12-16), along with seven known analogues (6-11 and 17), were isolated from the culture broth and the mycelia of Alternaria sp. ZJ-2008003, a fungus obtained from a Sarcophyton sp. soft coral collected from the South China Sea. Their structures and the relative configurations were elucidated using comprehensive spectroscopic methods including 1D and 2D NOE spectra as well as single-crystal X-ray crystallography. Compound 13 represents the first isolated alterporriol dimer with a C-4-C-4' linkage, and the absolute configuration of 4 was determined using the modified Mosher's method. Compounds 1 and 15 exhibited antiviral activity against the porcine reproductive and respiratory syndrome virus (PRRSV), with IC₅₀ values of 65 and 39 μM, respectively. Compound 14 showed cytotoxic activity against PC-3 and HCT-116 cell lines, with IC₅₀ values of 6.4 and 8.6 μM, respectively.

Chromophenazines from the Terrestrial Streptomyces sp. Ank 315

The new chromophenazines A-F [9-methyl-5-(3'-methylbut-2'-enyl)-5H-benzo[a]phenazin-7-one (1a), 9-methyl-5-(3'-methylbut-2'-enyl)-7-oxo-5,7-dihydrobenzo[a]phenazine-1-carboxylic acid (1b), 5-(3'-methylbut-2'-enyl)-7-oxo-5,7-dihydrophenazine-1-carboxamide (2), 3-benzoyl-5-(3'-methylbut-2'-enyl)-5,10-dihydrophenazine-1-carboxylic acid (5a), 3,7-dibenzoyl-5-(3'-methylbut-2'-enyl)-5,10-dihydrophenazine-1-carboxylic acid (5b), and 3,7-dibenzoyl-5-(3'-methylbut-2'-enyl)-5,10-dihydrophenazine-1-carboxamide (5c)], together with phenazine-1-carboxylic acid, 1-phenazinecarboxamide, 1-phenazinol, tryptophol, and anthranilic acid, were isolated from Streptomyces sp. Ank 315. The structures of the new compounds were established on the basis of spectroscopic data, 1D NOE, 2D NMR, and ESIMS measurements and comparison with literature values.

Molecular Hydrogen Tweezers: Structure and Mechanisms by Neutron Diffraction, NMR, and Deuterium Labeling Studies in Solid and Solution

The mechanism of reversible hydrogen activation by ansa-aminoboranes, 1-N-TMPH-CH(2)-2-[HB(C(6)F(5))(2)]C(6)H(4) (NHHB), was studied by neutron diffraction and thermogravimetric mass-spectroscopic experiments in the solid state as well as with NMR and FT-IR spectroscopy in solution. The structure of the ansa-ammonium borate NHHB was determined by neutron scattering, revealing a short N-H···H-B dihydrogen bond of 1.67 Å. Moreover, this intramolecular H-H distance was determined in solution to be also 1.6-1.8 Å by (1)H NMR spectroscopic T(1) relaxation and 1D NOE measurements. The X-ray B-H and N-H distances deviated from the neutron and the calculated values. The dynamic nature of the molecular tweezers in solution was additionally studied by multinuclear and variable-temperature NMR spectroscopy. We synthesized stable, individual isotopic isomers NDDB, NHDB, and NDHB. NMR measurements revealed a primary isotope effect in the chemical shift difference (p)Δ(1)H(D) = δ(NH) - δ(ND) (0.56 ppm), and hence supported dihydrogen bonding. The NMR studies gave strong evidence that the structure of NHHB in solution is similar to that in the solid state. This is corroborated by IR studies providing clear evidence for the dynamic nature of the intramolecular dihydrogen bonding at room temperature. Interestingly, no kinetic isotope effect was detected for the activation of deuterium hydride by the ansa-aminoborane NB. Theoretical calculations attribute this to an "early transition state". Moreover, 2D NOESY NMR measurements support fast intermolecular proton exchange in aprotic CD(2)Cl(2) and C(6)D(6).

Stereochemical Analysis of Leubethanol, an Anti-TB-Active Serrulatane, fromLeucophyllum frutescens

Bioactivity-guided fractionation of the methanolic root bark extract of Leucophyllum frutescens led to the identification of leubethanol (1), a new serrulatane-type diterpene with activity against both multi-drug-resistant and drug-sensitive strains of virulent Mycobacterium tuberculosis. Leubethanol (1) was identified by 1D/2D NMR data, as a serrulatane closely related to erogorgiane (2), and exhibited anti-TB activity with minimum inhibitory concentrations in the range 6.25-12.50 μg/mL. Stereochemical evidence for 1 was gleaned from 1D and 2D NOE experiments, from 1H NMR full spin analysis, and by comparison of the experimental vibrational circular dichroism (VCD) spectrum to density functional theory calculated VCD spectra of two diastereomers.

Novel O-glycosidic gossypol isomers and their bioactivities

Novel glycosidic gossypol analogs, 7,7′-gossypol diglucoside tetraacetate GS1, 6,7′-gossypol diglucoside tetraacetate GS2, 7,7′-gossypol diglycoside GS1′, 6,7′-gossypol diglycoside GS2′ were obtained by the ultrasound-assisted reaction of the potassium salt of gossypol with 2,3,4,6-tetra- O-acetyl-α- d-glucopyranosyl bromide under PTC conditions and were fully characterized by 1D NMR ( 1H NMR, 13C NMR, DEPT, 1D NOE), 2D NMR (HMBC, HMQC), FTIR, HRMS and HPLC. The anticancer activities, cytotoxic effects as well as anti-trypanosomal activities of these novel glycosidic gossypols were explored and suggest that gossypol glycosides could be used to develop new candidates for anticancer drugs and anti-trypanosomal agents.

Host−Guest Chemistry of Dendrimer−Drug Complexes. 6. Fully Acetylated Dendrimers as Biocompatible Drug Vehicles Using Dexamethasone 21- Phosphate as a Model Drug

Fully acetylated poly(amidoamine) (PAMAM) dendrimer was proposed as a biocompatible drug vehicle using dexamethasone 21-phosphate (Dp21) as a model drug. NMR techniques including (1)H NMR and 2D NOE NMR were used to characterize the host-guest chemistry of acetylated dendrimer/Dp21 and cationic dendrimer/Dp21 complexes. The pH-dependent micellization, complexation, and inclusion behaviors of Dp21 were observed in the presence of acetylated and cationic PAMAM dendrimers. Acetylated dendrimer only encapsulates Dp21 at acidic conditions, while cationic dendrimer can host Dp21 at both acidic and neutral conditions. The orientation of Dp21 molecules in the dendrimer cavities depends on the quaternization degree of tertiary amine groups of dendrimer and the protonation ratio of phosphate group of Dp21. A distinctive pH-dependent release behavior of Dp21 from the acetylated and nonacetylated dendritic matrix was observed: Dp21 exhibits a much slower release rate from acetylated dendrimer at lower pH conditions and a much faster release rate from nonacetylated dendrimer with decreasing pH values. Cytotoxicity studies further confirmed the biocompatibility of acetylated dendrimers, which are much safer in the delivery of therapeutics for the treatment of various diseases than nonacetylated dendrimers. The dendrimer-drug binding and release mechanisms provide a new insight for the design and optimization of biocompatible dendrimer-based drug delivery systems.

Molecular properties of mono guest-modified cyclodextrins on the secondary site

Novel guest-modified α- and β-cyclodextrins (CyDs) through an alkyl chain and amide bond (1 α, 2 α, 3 α, 2 β and 3 β) were synthesised in satisfactory yield (81–93%) by DCC condensation between 3-monoamino-3-monodeoxy-CyD and benzoic acid, phenylpropionic acid and phenylbutylic acid, respectively. These substituted CyDs include their phenyl groups into their own cavities, forming intra-molecular host–guest complexes evidenced by varied concentration of 1D and 2D NOE NMR spectra. Compounds 1–3 exhibit higher water solubility than native CyD.

Configurations and conformations of glycosyl sulfoxides

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

ChemInform Abstract: Structure Determination of Tigridial, an Iridopentaene from Tigridia pavonia (Iridaceae).

Besides numerous known iridals, which are unusual mono- or bicyclic triterpenoids of Iridaceae, lipid extracts of Tigridia pavonia bulbs contain tigridial (17), a new spirobicyclic hemiacetal with a conjugated pentaene moiety in the terpenoid side chain. The isolated natural product decomposes rapidly despite exclusion of light and oxygen. In contrast, derivatives of 17 formed by Diels–Alder reaction with 4-phenyl-3H-1,2,4-triazole-3,5-(4H)-dione (13) are stable, as are the products of a subsequent reduction with NaBH4. The products 15a,b and 16a,b of this reaction sequence were isolated and their structures elucidated by spectroscopic techniques. From these results structure 17 was inferred for the new natural product, which was confirmed by 1D and 2D NMR spectroscopy of a mixture of 11 and 17, in which the latter had been stabilized by addition of hydroquinone. The stereochemistry of 17 was deduced from 2D NOE experiments and comparison with known compounds.

Synthesis of mono- and dihydroxy-substituted 2-aminocyclooctanecarboxylic acid enantiomers

(1 R,2 S,6 R)-2-Amino-6-hydroxycyclooctanecarboxylic acid (−)- 10 was synthesized from (1 R,2 S)-2-aminocyclooct-5-enecarboxylic acid (+)- 2 via an iodolactone intermediate, while (1 R,2 S,3 R,4 S)-2-amino-5,6-dihydroxycyclooctanecarboxylic acid (−)- 12 was prepared by using the OsO 4-catalyzed oxidation of Boc-protected amino ester (−)- 5. The stereochemistry and relative configurations of the synthesized compounds were determined by 1D and 2D NMR spectroscopy (based on 2D NOE cross-peaks and 3 J(H,H) coupling constants) and X-ray crystallography.

Synthesis and conformational analysis of carbasugar bioisosteres of α- l-iduronic acid and its methyl glycoside

The synthesis of two novel carbasugar analogues of α- l-iduronic acid is described in which the ring-oxygen is replaced by a methylene group. In analogy with the conformational equilibrium described for α- l-Ido pA, the conformation of the carbasugars was investigated by 1H and 13C NMR spectroscopy. Hadamard transform NMR experiments were utilised for rapid acquisition of 1H, 13C-HSQC spectra and efficient measurements of heteronuclear long-range coupling constants. Analysis of 1H NMR chemical shifts and J H,H coupling constants extracted by a total-lineshape fitting procedure in conjunction with J H,C coupling constants obtained by three different 2D NMR experiments, viz., 1H, 13C-HSQC-HECADE, J-HMBC and IPAP-HSQC-TOCSY-HT, as well as effective proton–proton distances from 1D 1H, 1H T-ROE and NOE experiments showed that the conformational equilibrium 4 C 1⇌ 2 S 5a⇌ 1 C 4 is shifted towards 4 C 1 as the predominant or exclusive conformation. These carbasugar bioisosteres of α- l-iduronic acid do not as monomers show the inherent flexibility that is anticipated to be necessary for biological activity.

Absolute configurations of tubulin inhibitors taltobulin (HTI-286) and HTI-042 characterized by X-ray diffraction analysis and NMR studies

The stereochemistry of the tubulin inhibitors taltobulin HTI-286 ( 2) and HTI-042 ( 3) was determined by utilizing the DPFGSE 1D NOE experiment. Single crystal X-ray diffraction analysis further confirmed the absolute configuration of these two compounds, which carry the ( S, S, S)-configuration necessary for biological activity.

Complete assignments of 1H and 13C NMR data of three new dihydrophenanthrofurans from Pleione yunnanensis

Three new dihydrophenanthrofurans, pleionesins A-C (1-3), together with two known dihydrophenanthrenes (4-5) were isolated from the tubers of Pleione yunnanensis (Rolfe). The complete (1)H and (13)C NMR spectra assignments of these compounds were carried out using 1D and 2D NMR experiments ((1)H, (13)C, selective 1D NOE, HSQC and HMBC).

Complete 1H and 13C NMR data assignment of new constituents from Severinia buxifolia

Phytochemical analysis of different organs of the rutaceaeous plant Severinia buxifolia led to the isolation of a new limonoid, a new acridone alkaloid, and a new flavone. Structure elucidation and signal assignment were achieved by the extensive use of 1D and 2D NMR experiments (selective 1D NOE, COSY, NOESY, HSQC, HMBC).