A site-specific low-enrichment (15)N,(13)C isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acids

We demonstrate that base and sugar protons within a DNA oligomer can be assigned unambiguously following site-specific 15N,13C isotope incorporation at levels as low as 1% enrichment. This simple and cost-effective methodology is demonstrated on the d(GGGTTCAGG) DNA sequence, which forms a dimeric G-quadruplex containing G.G.G.G tetrads sandwiched between G.(C-A) triads.     

Characterization of (1)H-(1)H distances in a uniformly (2)H,(15)N-labeled SH3 domain by MAS solid-state NMR spectroscopy (section sign)

In this communication, we demonstrate the feasibility of obtaining long-range (1)H-(1)H distance information by MAS solid-state NMR for a microcrystalline, uniformly (2)H,(15)N-labeled sample of a SH3 domain of chicken alpha-spectrin. The experiments yield NOESY-type spectra and rely on the favorable dispersion of the (15)N chemical shifts of the protein backbone. Perdeuteration of nonexchangeable sites is employed to simplify proton spin systems and to obtain multiple structural information. Two mixing schemes, (1)H-(1)H double quantum filtered Post-C7 and (1)H spin diffusion, are implemented to obtain quantitative (1)H-(1)H distance information. Post-C7 and spin diffusion cross-peak buildup rates are discussed for initial-rate fitting and in the framework of n = 0 rotational resonance (rotor driven spin diffusion), respectively. Different deuteration schemes were tested to find conditions where short-range (1)H-(1)H interactions are truncated (e.g., between H(N) and H(alpha)), but long-range interactions are retained (e.g., between H(N) and H(N)).     

Determination of multiple torsion-angle constraints in U-(13)C,(15)N-labeled peptides: 3D (1)H-(15)N-(13)C-(1)H dipolar chemical shift NMR spectroscopy in rotating solids

We demonstrate constraint of peptide backbone and side-chain conformation with 3D (1)H-(15)N-(13)C-(1)H dipolar chemical shift, magic-angle spinning NMR experiments. In these experiments, polarization is transferred from (15)N[i] by ramped SPECIFIC cross polarization to the (13)C(alpha)[i], (13)C(beta)[i], and (13)C(alpha)[i - 1] resonances and evolves coherently under the correlated (1)H-(15)N and (1)H-(13)C dipolar couplings. The resulting set of frequency-labeled (15)N(1)H-(13)C(1)H dipolar spectra depend strongly upon the molecular torsion angles phi[i], chi1[i], and psi[i - 1]. To interpret the data with high precision, we considered the effects of weakly coupled protons and differential relaxation of proton coherences via an average Liouvillian theory formalism for multispin clusters and employed average Hamiltonian theory to describe the transfer of (15)N polarization to three coupled (13)C spins ((13)C(alpha)[i], (13)C(beta)[i], and (13)C(alpha)[i - 1]). Degeneracies in the conformational solution space were minimized by combining data from multiple (15)N(1)H-(13)C(1)H line shapes and analogous data from other 3D (1)H-(13)C(alpha)-(13)C(beta)-(1)H (chi1), (15)N-(13)C(alpha)-(13)C'-(15)N (psi), and (1)H-(15)N[i]-(15)N[i + 1]-(1)H (phi, psi) experiments. The method is demonstrated here with studies of the uniformly (13)C,(15)N-labeled solid tripeptide N-formyl-Met-Leu-Phe-OH, where the combined data constrains a total of eight torsion angles (three phi, three chi1, and two psi): phi(Met) = -146 degrees, psi(Met) = 159 degrees, chi1(Met) = -85 degrees, phi(Leu) = -90 degrees, psi(Leu) = -40 degrees, chi1(Leu) = -59 degrees, phi(Phe) = -166 degrees, and chi1(Phe) = 56 degrees. The high sensitivity and dynamic range of the 3D experiments and the data analysis methods provided here will permit immediate application to larger peptides and proteins when sufficient resolution is available in the (15)N-(13)C chemical shift correlation spectra.     

Heteronuclear NMR spectroscopy for lysine NH(3) groups in proteins: unique effect of water exchange on (15)N transverse relaxation

In this paper, we present a series of heteronuclear NMR experiments for the direct observation and characterization of lysine NH3 groups in proteins. In the context of the HoxD9 homeodomain bound specifically to DNA we were able to directly observe three cross-peaks, arising from lysine NH3 groups, with 15N chemical shifts around approximately 33 ppm at pH 5.8 and 35 degrees C. Measurement of water-exchange rates and various types of 15N transverse relaxation rates for these NH3 groups, reveals that rapid water exchange dominates the 15N relaxation for antiphase coherence with respect to 1H through scalar relaxation of the second kind. As a consequence of this phenomenon, 15N line shapes of NH3 signals in a conventional 1H-15N heteronuclear single quantum coherence (HSQC) correlation experiment are much broader than those of backbone amide groups. A 2D 1H-15N correlation experiment that exclusively observes in-phase 15N transverse coherence (termed HISQC for heteronuclear in-phase single quantum coherence spectroscopy) is independent of scalar relaxation in the t(1) (15N) time domain and as a result exhibits strikingly sharper 15N line shapes and higher intensities for NH3 cross-peaks than either HSQC or heteronuclear multiple quantum coherence (HMQC) correlation experiments. Coherence transfer through the relatively small J-coupling between 15Nzeta and 13Cepsilon (4.7-5.0 Hz) can be achieved with high efficiency by maintaining in-phase 15N coherence owing to its slow relaxation. With the use of a suite of triple resonance experiments based on the same design principles as the HISQC, all the NH3 cross-peaks observed in the HISQC spectrum could be assigned to lysines that directly interact with DNA phosphate groups. Selective observation of functional NH3 groups is feasible because of hydrogen bonding or salt bridges that protect them from rapid water exchange. Finally, we consider the potential use of lysine NH3 groups as an alternative probe for larger systems as illustrated by data obtained on the 128-kDa enzyme I dimer.     

1H, 13C and 15N NMR spectra of ciprofloxacin

1H NMR assignment, including the values of delta(H) and J(H,H) for the cyclopropane moiety, and 13C NMR and 15N NMR spectral data for ciprofloxacin are presented.     

1H, 13C and 15N NMR assignments of phenazopyridine derivatives

Phenazopyridine hydrochloride (1), a drug in clinical use for many decades, and some derivatives were studied by one- and two-dimensional (1)H, (13)C and (15)N NMR methodology. The assignments, combined with DFT calculations, reveal that the preferred protonation site of the drug is the pyridine ring nitrogen atom. The chemoselective acetylation of phenazopyridine (2) and its influence on the polarization of the azo nitrogen atoms were evidenced by the (15)N NMR spectra. Molecular calculations of the phenazopyridines 2-4 show that the pyridine and phenyl groups are oriented in an antiperiplanar conformation with intramolecular hydrogen bonding between the N-b atom and the C-2 amino group preserving the E-azo stereochemistry.     

2D relayed15N,1H correlated NMR spectroscopy of a pentadecapeptide at natural abundance of15N

Summary Proton-detected H-relayed N,H correlation NMR spectroscopy at natural abundance of¹⁵N has been used to demonstrate the enormous value of heteronuclear NMR spectroscopy for the proton assignment of medium-sized oligopeptides.

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Zweidimensionalerelayed ¹⁵N,¹H-korrelierte NMR-Spektroskopie an einem Pentadecapeptid bei natürlicher Häufigkeit von¹⁵N

Zusammenfassung Anhand¹H-detektierterrelayed-N,H-korrelierter NMR-Spektroskopie bei natürlicher Häufigkeit von¹⁵N wird die große Bedeutung der heteronuklearen Kernresonanzspektroskopie für die Protonenzuordnung mittlerer Oligopeptide demonstriert.

     

1H, 13C and 15N NMR spectra of [1,2-15N2]pyrazole derivatives

The chemical shifts and coupling constants of [1,2-¹⁵N₂]pyrazole, 2-(1-[1,2- ¹⁵N₂]pyrazolyl)-2-[l,3-²H₆]propanol, 1-nitro[1,2¹⁵N₂] and 3-nitro[1,2-¹⁵N₂]pyrazole are reported.     

Multinuclear NMR (1H,13C,15N,17O) studies of intramolecular interactions in 1-vinylpyridones and quinolones

¹H and¹³C NMR was used to estimate the dihedral angles between the planes of the vinyl group and the hetero ring for 1-vinylpyridones and quinolones. The¹H,¹³C,¹⁵N, and¹⁷O NMR data showed the existence of a specific intramolecular weak hydrogen bond between the -H atom of the vinyl group and the O atom in 1-vinyl-2-pyridones and 2-vinyl-1-isoquinolone.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 7, pp. 1539–1547, July, 1990.     

1H, 13C and 15N NMR spectroscopy and tautomerism of nitrobenzotriazoles

Benzotriazole nitro derivatives were prepared by nitration of the corresponding benzotriazoles and by methylation or cyclization of appropriate nitro‐1,2‐phenylenediamines. Structures and tautomerism of the nitrobenzotriazoles were studied by multinuclear ¹H, ¹³C, ¹⁵N, and 2D NMR spectroscopy and quantum chemistry. Copyright © 2008 John Wiley & Sons, Ltd.     

NMR studies in the heterocyclic series XXIV—1H, 13C and 15N study of 15N labelled indazoles

The ¹⁵N chemical shifts and ¹H? ¹⁵N and ¹³C? ¹⁵N coupling constants of nine monolabelled indazoles were measured and assigned. The experimental values are discussed in terms of the indazolic and iso-indazolic structures, and compared with literature data for other related heterocycles. All the results are consistent with an N-1(H) tautomeric structure for indazole in DMSO-d₆.     

1H, 13C, 15N NMR and IR Spectroscopic Studies of a Rh(II) Complex of Thiourea

A rhodium(II) complex of thiourea (Tu), Rh₂(OAc)₄Tu₂, has been prepared from Rh₂(OAc)₄(H₂O)₂ and characterized. A shift of the ν(N?H) vibration towards higher frequencies in the IR spectrum is consistent with sulfur coordination to rhodium(II). ¹³C NMR spectra recorded in DMSO-d ₆ reveal that thiourea is replaced by DMSO-d ₆ solvent, followed by replacement of acetate ions by free thiourea. ¹⁵N NMR indicates some nitrogen involvement in coordination to form an S?N chelate.     

1H, 13C,and 15N NMR spectra of some pyridazine derivatives

¹H, ¹³C, and ¹⁵N NMR chemical shifts for pyridazines 4–22 were measured using 1D and 2D NMR spectroscopic methods including ¹H? ¹H gDQCOSY, ¹H? ¹³C gHMQC, ¹H? ¹³C gHMBC, and ¹H? ¹⁵N CIGAR–HMBC experiments. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical study of bifurcated hydrogen bonding effects on the 1J(N,H), 1hJ(N,H), 2hJ(N,N) couplings and 1H, 15N shieldings in model pyrroles

According to the density functional theory calculations, the X···H···N (X?N, O) intramolecular bifurcated (three‐centered) hydrogen bond with one hydrogen donor and two hydrogen acceptors causes a significant decrease of the ^1hJ(N,H) and ^2hJ(N,N) coupling constants across the N? H···N hydrogen bond and an increase of the ¹J(N,H) coupling constant across the N? H covalent bond in the 2,5‐disubsituted pyrroles. This occurs due to a weakening of the N? H···N hydrogen bridge resulting in a lengthening of the N···H distance and a decrease of the hydrogen bond angle at the bifurcated hydrogen bond formation. The gauge‐independent atomic orbital calculations of the shielding constants suggest that a weakening of the N? H···N hydrogen bridge in case of the three‐centered hydrogen bond yields a shielding of the bridge proton and deshielding of the acceptor nitrogen atom. The atoms‐in‐molecules analysis shows that an attenuation of the ^1hJ(N,H) and ^2hJ(N,N) couplings in the compounds with bifurcated hydrogen bond is connected with a decrease of the electron density ρ_H···N at the hydrogen bond critical point and Laplacian of this electron density ?²ρ_H···N. The natural bond orbital analysis suggests that the additional N? H···X interaction partly inhibits the charge transfer from the nitrogen lone pair to the σ*_{N? H} antibonding orbital across hydrogen bond weakening of the ^1hJ(N,H) and ^2hJ(N,N) trans‐hydrogen bond couplings through Fermi‐contact mechanism. An increase of the nitrogen s‐character percentage of the N? H bond in consequence of the bifurcated hydrogen bonding leads to an increase of the ¹J(N,H) coupling constant across the N? H covalent bond and deshielding of the hydrogen donor nitrogen atom. Copyright © 2010 John Wiley & Sons, Ltd.     

Complete (1)H NMR spectral fingerprint of huperzine A

Complete analysis of the (1)H NMR spectrum of huperzine A, 1-amino-13-ethylidene-11-methyl-6-aza-tricyclo[7.3.1.0(2, 7)]trideca-2(7),3,10-trien-5-one, a Lycopodium alkaloid and anti-Alzheimer drug lead containing an ABCD(E)(MN)(OP)X(3)Y(3)-type system of 15 nonexchangeable proton spins, is reported for the first time, and earlier assignments are corrected. The complete (1)H parameter set of 11 chemical shifts clarifies the diastereotopism of both methylene groups, and provides a total of 38 observed H,H-couplings including 31 long-range ((4-6)J) connectivities. The NMR data is consistent with the comparatively rigid alicyclic backbone predicted by molecular mechanics calculations, and forms the basis for (1)H NMR fingerprint analysis for the purpose of dereplication, purity analysis, and elucidation of structural analogs.     

A 15N NMR study of some azoles

¹⁵N NMR data are reported for 42 azoles, taken mostly at a standard concentration and in a common solvent (0.5 M dimethyl sulfoxide with a 0.01 M increment of Cr(acac)₃ for each nitrogen atom present). Signal assignments were assisted by comparison with ¹⁴N line widths, the use of ²J(¹⁵N¹H) couplings, and shielding calculations obtained by the INDO/S–SOS approach. The generally large differences in nitrogen-shielding changes permitted rather facile shift assignments.     

1H, 13C and 15N NMR spectral assignments for new triazapentalene derivatives

Mesomeric heteropentalene betaines are conjugated fused polyheterocyclic structures that represent interesting intermediates for organic synthesis. Five such structures, containing at least four nitrogen atoms and various substituents, have been characterized by ¹H, ¹³C and ¹⁵N NMR. We report, apparently for the first time, nitrogen NMR data and coupling information on such systems. Inter‐ring long‐range correlations across five bonds with ¹⁵N (⁵J_HN) and up to seven bonds with ¹³C (⁶J_HC and ⁷J_HC) were observed in HSQC experiments. The incorporation of an electron‐withdrawing substituent such as NO₂ was observed to cause an increase in the magnitude of the remote couplings and deshielding of nearby protons, carbons and on all nitrogen atoms of the structure, including remote ones situated on other cycles. Copyright © 2009 John Wiley & Sons, Ltd.