Magnitudes and Orientations of the N Chemical Shift Tensor of [1-N]-2′-Deoxyguanosine Determined on a Polycrystalline Sample by Two-Dimensional Solid-State NMR Spectroscopy

The magnitudes and orientations of the ¹⁵N chemical shift tensor of [1-¹⁵N]-2′-deoxyguanosine were determined from a polycrystalline sample using the two-dimensional PISEMA experiment. The magnitudes of the principal values of the ¹⁵N chemical shift tensor of the N1 nitrogen of [1-¹⁵N]-2′-deoxyguanosine were found to be ς₁₁ = 54 ppm, ς₂₂ = 148 ppm, and ς₃₃ = 201 ppm with respect to (¹⁵NH₄)₂SO₄ in aqueous solution. Comparisons of experimental and simulated two-dimensional powder pattern spectra show that ς_33N is approximately collinear with the N–H bond. The tensor orientation of ς_33N for N1 of [1-¹⁵N]-2′-deoxyguanosine is similar to the values obtained for the side chain residues of ¹⁵N_ε1-tryptophan and ¹⁵N_π-histidine even though the magnitudes differ significantly.     

Measurement of 15N chemical shift anisotropy in a protein dissolved in a dilute liquid crystalline medium with the application of magic angle sample spinning

The chemical shifts of nuclei that have chemical shielding anisotropy, such as the 15N amide in a protein, show significant changes in their chemical shifts when the sample is altered from an isotropic state to an aligned state. Such orientation-dependent chemical shift changes provide information on the magnitudes and orientation of the chemical shielding tensors relative to the molecule's alignment frame. Because of the extremely high sensitivity of the chemical shifts to the sample conditions, the changes in chemical shifts induced by adding aligned bicelles do not arise only from the protein alignment but should also include the accumulated effects of environmental changes including protein-bicelle interactions. With the aim of determining accurate 15N chemical shielding tensor values for solution proteins, here we have used magic angle sample spinning (MAS) to observe discriminately the orientation-dependent changes in the 15N chemical shift. The application of MAS to an aligned bicelle solution removes the torque that aligns the bicelles against the magnetic field. Thus, the application of MAS to a protein in a bicelle solution eliminates only the molecular alignment effect, while keeping all other sample conditions the same. The observed chemical shift differences between experiments with and without MAS therefore provide accurate values of the orientation-dependent 15N chemical shifts. From the values for ubiquitin in a 7.5% (w/v) bicelle medium, we determined the 15N chemical shielding anisotropy (CSA) tensor. For this evaluation, we considered uncertainties in measuring the 1H-15N dipolar couplings and the 15N chemical shifts and also structural noise present in the reference X-ray structure, assuming a random distribution of each NH bond vector in a cone with 5 degrees deviation from the original orientation. Taking into account these types of noise, we determined the average 15N CSA tensor for the residues in ubiquitin as Delta sigma=-162.0+/-4.3 ppm, eta=0.18+/-0.02, and beta=18.6+/-0.5 degrees, assuming a 1H-15N bond length of 1.02 A. These tensor values are consistent with those obtained from solid-state NMR experiments.     

Adducts of rhodium(II) tetraacetate with some nitrogenous organic ligands: application of natural abundance 15N and 13C CPMAS NMR spectroscopy

Adducts of rhodium(II) tetraacetate with some nitrogenous organic ligands: 1-azabicyclo[2,2,2]octane 1, 1,2-diazabicyclo[2,2,2]octane 2, pyrazine 3, pyrimidine 4, [1,3,5]triazine 5 and 1,3,5,7-tetraazatricyclo[3,3,1,1(3,7)]decane 6 have been investigated by means of natural abundance (13)C and (15)N CPMAS nuclear magnetic resonance (NMR) spectroscopy. 1-Azabicyclo[2,2,2]octane 1 having one nitrogen atom in the molecule produces either the 1:1 or 1:2-adduct depending on the reagent molar ratio; some features of its (13)C CPMAS NMR spectra suggest the dimeric structure of the 1:1-adduct. Multifunctional ligands having more than one nitrogen atom in a molecule yield the adducts insoluble in common organic solvents. Elemental analysis and NMR experiments have revealed that 1,2-diazabicyclo[2,2,2]octane, pyrazine, pyrimidine and [1,3,5]triazine produced adducts in the form of 1:1 polymeric chains. 1,3,5,7-tetraazatricyclo[3,3,1,1(3,7)]decane yields the adduct containing ligand and metal salt in the molar ratio of 3:4. The (15)N chemical shift change caused by the Rh-N bond formation (Deltadelta parameter) varies from ca. -9 ppm for aliphatic ligands to ca. -40 ppm for heteroaromatic species. The NMR findings have been supported by theoretical calculation (density functional calculation (DFT), LanLD2Z//B3LYB level) of molecular geometry, energy and chemical shieldings.     

Insight into the CSA tensors of nucleobase carbons in RNA polynucleotides from solution measurements of residual CSA: towards new long-range orientational constraints

Using residual chemical shift anisotropies (RCSAs) measured in a weakly aligned stem-loop RNA, we examined the carbon chemical shift anisotropy (CSA) tensors of nucleobase adenine C2, pyrimidine C5 and C6, and purine C8. The differences between the measured RCSAs and the values back-calculated using three nucleobase carbon CSA sets [D. Stueber, D.M. Grant, 13C and 15N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551; D. Sitkoff, D.A. Case, Theories of chemical shift anisotropies in proteins and nucleic acids, Prog. NMR Spectrosc. 32 (1998) 165-190; R. Fiala, J. Czernek, V. Sklenar, Transverse relaxation optimized triple-resonance NMR experiments for nucleic acids, J. Biomol. NMR 16 (2000) 291-302] reported previously for mononucleotides (1.4 Hz) is significantly smaller than the predicted RCSA range (-10-10 Hz) but remains larger than the RCSA measurement uncertainty (0.8 Hz). Fitting of the traceless principal CSA values to the measured RCSAs using a grid search procedure yields a cytosine C5 CSA magnitude (CSAa=(3/2.(delta11(2)+delta22(2)+delta33(2)))1/2=173+/-21 ppm), which is significantly higher than the reported mononucleotide values (131-138 ppm) and a guanine C8 CSAa (148+/-13 ppm) that is in very good agreement with the mononucleotide value reported by solid-state NMR [134 ppm, D. Stueber, D.M. Grant, 13C and (15)N chemical shift tensors in adenosine, guanosine dihydrate, 2'-deoxythymidine, and cytidine, J. Am. Chem. Soc. 124 (2002) 10539-10551]. Owing to a unique sensitivity to directions normal to the base plane, the RCSAs can be translated into useful long-range orientational constraints for RNA structure determination even after allowing for substantial uncertainty in the nucleobase carbon CSA tensors.     

207Pb NMR of minium, Pb3O4: evidence for the [Pb2]4+ ion and possible relativistic effects in the Pb-Pb bond

Solid Pb3O4 has been studied with 207Pb nuclear magnetic resonance (NMR) spectroscopy. The 207Pb NMR chemical-shift tensor of the Pb2+ site has principal values of delta11 = 1980 +/- 5 ppm, delta22 = 1540 +/- 5 ppm, and delta33 = -1108 +/- 10 ppm; delta(iso) = 804 +/- 10 ppm. The chemical-shift tensor of the Pb4+ site is axial, with principal values delta(parallel) = -1009 +/- 3 ppm and delta(perpendicular) = 1132 +/- 3 ppm; delta(iso) = -1091 +/- 3 ppm. The Pb4+-Pb2+ scalar coupling constant J(Pb-Pb) = 2.3 +/- 0.1 kHz. The main contribution to the Pb2- chemical-shift anisotropy is proposed to arise from an exchange interaction in the Pb2+-Pb2+ pairs, conventionally regarded as molecular [Pb2]4+ ions.     

15N chemical shift tensor magnitude and orientation in the molecular frame of uracil determined via MAS NMR

The potential of heteronuclear MAS NMR spectroscopy for the characterization of (15)N chemical shift (CS) tensors in multiply labeled systems has been illustrated, in one of the first studies of this type, by a measurement of the chemical shift tensor magnitude and orientation in the molecular frame for the two (15)N sites of uracil. Employing polycrystalline samples of (15)N(2) and 2-(13)C, (15)N(2)-labeled uracil, we have measured, via (15)N-(13)C REDOR and (15)N-(1)H dipolar-shift experiments, the polar and azimuthal angles (θ, psi) of orientation of the (15)N-(13)C and (15)N-(1)H dipolar vectors in the (15)N CS tensor frame. The (θ(NC), psi(NC)) angles are determined to be (92 +/- 10 degrees, 100 +/- 5 degrees ) and (132 +/- 3 degrees, 88 +/- 10 degrees ) for the N1 and N3 sites, respectively. Similarly, (θ(NH), psi(NH)) are found to be (15 +/- 5 degrees, -80 +/- 10 degrees ) and (15 +/- 5 degrees, 90 +/- 10 degrees ) for the N1 and N3 sites, respectively. These results obtained based only on MAS NMR measurements have been compared with the data reported in the literature.     

15N chemical shift referencing in solid state NMR

Solid-state NMR spectroscopy has much advanced during the last decade and provides a multitude of data that can be used for high-resolution structure determination of biomolecules, polymers, inorganic compounds or macromolecules. In some cases the chemical shift referencing has become a limiting factor to the precision of the structure calculations and we have therefore evaluated a number of methods used in proton-decoupled ¹⁵N solid-state NMR spectroscopy. For ¹³C solid-state NMR spectroscopy adamantane is generally accepted as an external standard, but to calibrate the ¹⁵N chemical shift scale several standards are in use. As a consequence the published chemical shift values exhibit considerable differences (up to 22 ppm). In this paper we report the ¹⁵N chemical shift of several commonly used references compounds in order to allow for comparison and recalibration of published data and future work. We show that ¹⁵NH₄Cl in its powdered form (at 39.3 ppm with respect to liquid NH₃) is a suitable external reference as it produces narrow lines when compared to other reference compounds and at the same time allows for the set-up of cross-polarization NMR experiments. The compound is suitable to calibrate magic angle spinning and static NMR experiments. Finally the temperature variation of ¹⁵NH₄Cl chemical shift is reported.     

One- and two-dimensional 15N exchange CP/MAS NMR studies of the structure and electronic properties of the intermolecular N-H...N hydrogen bond in imidazole crystal

The hydrogen bond of the type N-H...N in imidazole crystal has been studied by one and two-dimensional 15N exchange CP/MAS NMR measurements as well as the powder NMR spectrum. The chemical shift anisotropies for -N= and -N< were determined from the powder 1D spectrum. In 2D exchange CP/MAS NMR spectrum, the cross peaks between the 15N main resonance peaks for -N= and -N< were observed, implying that magnetization exchange between -N= and -N< takes place. The 1D exchange CP/MAS NMR measurements determined the exchange rate of magnetization at 289 K to be 1.3 and 1.5 s(-1) for -N= and -N<, respectively. The proton-driven spin-diffusion model interprets the experimental values, and the exchange rate depends strongly on the RF power of the proton decoupling field, suggesting that the magnetization transfer between -N= and -N< takes place by the 1H-driven spin-diffusion mechanism.     

Hydrogen bonding effects on the (15)N and (1)H shielding tensors in nucleic acid base pairs

The results of systematic ab initio calculations of (15)N and (1)H chemical shielding tensors in the GC base pair as a function of hydrogen bond length are presented for the first time. The hydrogen bond length characterized by the distance r(N...N) between purine N1 and pyrimidine N3 was varied between 2.57 and 3.50 A and the chemical shift tensors were calculated by the sum-over-states density functional perturbation theory. It is shown that the hydrogen bond length has a strong effect on the chemical shielding tensor of both imino proton and nitrogen, on their orientation, and, as a consequence, on the relaxation properties of both nuclei. For a nitrogen nucleus not involved in hydrogen bonding, the shielding tensor is nearly axially symmetric and almost collinear with the bond vector. As the length of the hydrogen bond decreases, the least shielding component sigma(11) deflects from the N-H vector and the shielding tensor becomes increasingly asymmetric. The significance of the presented results for the analysis of relaxation data and the efficiency of TROSY effects together with a summary of the relevant shielding parameters are presented and discussed.     

Sensitivity-enhanced static 15N NMR of solids by 1h indirect detection

A method for enhancing the sensitivity of 15N spectra of nonspinning solids through 1H indirect detection is introduced. By sampling the 1H signals in the windows of a pulsed spin-lock sequence, high-sensitivity 1H spectra can be obtained in two-dimensional (2D) spectra whose indirect dimension yields the 15N chemical shift pattern. By sacrificing the 1H chemical shift information, sensitivity gains of 1.8 to 2.5 for the 15N spectra were achieved experimentally. A similar sensitivity enhancement was also obtained for 2D (15)N-(1)H dipolar and 15N chemical shift correlation spectroscopy, by means of a 3D 1H/15N-1H/15N correlation experiment. We demonstrate this technique, termed PRINS for proton indirectly detected nitrogen static NMR, on a crystalline model compound with long 1H T(1rho) and on a 25-kDa protein with short 1H T(1rho). This 1H indirect detection approach should be useful for enhancing the sensitivity of 15N NMR of oriented membrane peptides. It can also be used to facilitate the empirical optimization of 15N-detected experiments where the inherent sensitivity of the sample is low.     

Orientational information from TEDOR spectral sidebands.

In a dipolar-coupled spin-1/2 network of the type 15N1-(13)C-15N2, an assessment of the sensitivity of the N --> C and C --> N TEDOR sideband intensities to the Euler angles defining the orientation of the two heteronuclear dipolar vectors in the 13C and 15N chemical shift (CS) tensor principal axes system has been carried out via numerical calculations. The results clearly indicate the potential of TEDOR MAS NMR spectroscopy for the characterization of the CS tensor orientation in the molecular frame. The efficacy of the method has been experimentally illustrated by TEDOR studies on a polycrystalline sample of [1, 3-(15)N2, 2-(13)C]uracil, which is one of the four bases in RNA.     

A standard for silver CP/MAS experiments

Silver methanesulfonate, AgSO3CH3, is a photo-stable, commercially available compound which is a superior 109Ag standard for setting up CP/MAS experiments. The 109Ag CP/MAS spectrum at moderate sample spinning speeds easily yields a single, relatively narrow peak with a single transient. The 109Ag chemical shift of solid AgSO3CH3 is 87.2 ppm with respect to a 9 M aqueous solution of AgNO3. The static spectrum yields chemical shift tensor components delta11=191 ppm, delta22=63 ppm and delta33=8 ppm. Therefore the span, Omega, is 183 ppm and the skew, kappa, is -0.39. These values are in accord with the known crystal structure.     

Characterization of 15N chemical shift tensors via 15N-13C REDOR and 1N-1H dipolar-shift CPMAS NMR spectroscopy

As part of our studies on the characterization of 15N chemical shift anisotropy (CSA) via magic angle spinning (MAS) NMR spectroscopy, we have investigated via numerical simulations the sensitivity of two different REDOR experimental protocols to the angles defining the orientation of the 15N-13C' bond vector in the principal axis system of the 15N CSA tensor of the amide nitrogen in a peptide bond. Additionally, employing polycrystalline samples of 15N and 13C', 15N-labeled acetanilide, we have obtained, in a first study of this type, the orientation of the 15N CSA tensor in the molecular frame by orienting the tensor with respect to the 15N-3C' and 15N-1H dipolar vectors via 15N-13C' REDOR and 15N-1H dipolar-shift MAS experiments, respectively.     

Determination of the 19F NMR chemical shielding tensor and crystal structure of 5-fluoro-dl-tryptophan

5-Fluoro-dl-tryptophan (5F-Trp) is a very sensitive probe used to investigate orientation and dynamics of biomacromolecules at the in situ level. In order to establish a (19)F NMR strategy, the crystal structure and (19)F chemical shielding tensor of 5F-Trp are reported. A novel approach was developed to use F-F homonuclear dipole-dipole coupling information to analyze single-crystal NMR data without determining crystal orientations. The measured values for the principal components of the shielding tensor are sigma(11)=0.9, sigma(22)=-63.3, and sigma(33)=-82.9 ppm relative to TFA in D(2)O. The principal axes of the shielding tensors coincide with the indole ring symmetry, which makes it a straightforward and powerful tool to monitor protein alignment in oriented environments. Hartree-Fock (HF) and density functional theory (DFT) calculations of the chemical shielding tensors are also reported.     

Determination of the 17O NMR tensors in potassium hydrogen dibenzoate: a salt containing a short O...H...O hydrogen bond

Solid-state 17O NMR spectra were obtained at 4.70, 11.75 and 19.60T for potassium hydrogen [17O(4)]dibenzoate (PHB) under both magic-angle spinning and stationary conditions. Spectral analyses yielded both the magnitude and orientation of the 17O chemical shift (CS) tensor and the electric field gradient (EFG) tensor for each of the two chemically distinct oxygen sites in PHB. For the oxygen site that is not involved in hydrogen bonding, the experimental 17O NMR tensors are: delta(iso)=287+/-2 ppm, delta(11)=470+/-5 ppm, delta(22)=380+/-5 ppm, delta(33)=10+/-5 ppm, C(Q)=8.30+/-0.02 MHz, eta(Q)=0.23+/-0.05, alpha=0+/-5 degrees, beta=90+/-5 degrees, and gamma=30+/-5 degrees. For the oxygen site in the short O...H...O hydrogen bond, the experimental 17O NMR tensors are: delta(iso)=213+/-2 ppm, delta(11)=370+/-5 ppm, delta(22)=190+/-5 ppm, delta(33)=80+/-5 ppm, C(Q)=5.90+/-0.02 MHz, eta(Q)=0.55+/-0.05, alpha=5+/-5 degrees, beta=90+/-5 degrees, and gamma=90+/-5 degrees. Extensive quantum mechanical calculations at both restricted Hartree-Fock and density functional theory levels were performed to investigate the effects of an effectively symmetrical O...H...O hydrogen bond on 17O CS and EFG tensors.     

Characterization of dynamic processes using deuterium in uniformly 2H,13C,15N enriched peptides by MAS solid-state NMR

We present in this paper 2H,13C MAS correlation experiments that are performed on a uniformly 2H,13C,15N labeled sample of Nac-Val, and on the uniformly 2H,15N labeled dipeptide Nac-Val-Leu-OH. The experiments involve the measurement of 2H T1 relaxation times at two different magnetic fields, as well as the measurement of the 2H tensor parameters by evolution of the 2H chemical shift. The data are interpreted quantitatively to differentiate between different side chain motional models.     

Carbon-13 and fluorine-19 NMR spectroscopy of the supramolecular solid p-tert-butylcalix(4)arene.alpha,alpha,alpha-trifluorotoluene

The supramolecular 1:1 host-guest inclusion compound, p-tert-butylcalix[4]arene x alpha,alpha,alpha-trifluorotoluene, 1, is characterized by 19F and 13C solid-state NMR spectroscopy. Whereas the 13C NMR spectra are easily interpreted in the context of earlier work on similar host-guest compounds, the 15F NMR spectra of solid 1 are, initially, more difficult to understand. The 19F[1H] NMR spectrum obtained under cross-polarization and magic-angle spinning conditions shows a single isotropic resonance with a significant spinning sideband manifold. The static 19F[1H] CP NMR spectrum consists of a powder pattern dominated by the contributions of the anisotropic chemical shift and the homonuclear dipolar interactions. The 19F MREV-8 experiment, which minimizes the 19F-19F dipolar contribution, helps to identify the chemical shift contribution as an axial lineshape. The full static 19F[1H] CP NMR spectrum is analysed using subspectral analysis and subsequently simulated as a function of the 19F-19F internuclear distance (D(FF) = 2.25 +/- 0.01 A) of the rapidly rotating CF3 group without including contributions from additional libration motions and the anisotropy in the scalar tensor. The shielding span is found to be 56 ppm. The width of the centerband in the 19F[1H] sample-spinning CP NMR spectrum is very sensitive to the angle between the rotor and the magnetic field. Compound 1 is thus an attractive standard for setting the magic angle for NMR probes containing a fluorine channel with a proton-decoupling facility.     

The 15N chemical shifts in mixed NB2Si and NBSi2 environments of Si3B3N7--a theoretical investigation

Nuclear magnetic resonance (NMR) chemical shifts in solids may be calculated by ab initio methods approximating the solid state by molecular clusters. We employed this technique to obtain estimates of (15)N chemical shifts in NB(2)Si and NBSi(2) environments in the solid state. Such nitrogen environments are found in amorphous (Si/B/N-)ceramics which exhibit very interesting features such as high thermal and mechanical stability. We based our calculations on cutouts of hypothetical Si(3)B(3)N(7) crystals suggested by Kroll and Hoffmann [Silicon boron nitrides: hypothetical polymorphs of Si(3)B(3)N(7), Angew. Chem. Int. Ed. 37 (1998) 2527]. Taking the systematic errors of our calculations into account we expect the chemical shifts in NBSi(2) environments around -293+/-5ppm. Chemical shifts in NB(2)Si environments are expected at -272+/-6ppm. The range of the calculated chemical shifts in NBSi(2) environments coincides with experimental chemical shifts in molecular compounds. Experimental chemical shifts of NB(2)Si nitrogen in molecules appear at lower field than our calculated chemical shifts in the solid state.     

Separation of anisotropy and exchange broadening using (15)N CSA-(15)N-(1)H dipole-dipole relaxation cross-correlation experiments

Based on the measurement of cross-correlation rates between (15)N CSA and (15)N-(1)H dipole-dipole relaxation we propose a procedure for separating exchange contributions to transverse relaxation rates (R(2) = 1/T(2)) from effects caused by anisotropic rotational diffusion of the protein molecule. This approach determines the influence of anisotropy and chemical exchange processes independently and therefore circumvents difficulties associated with the currently standard use of T(1)/T(2) ratios to determine the rotational diffusion tensor. We find from computer simulations that, in the presence of even small amounts of internal flexibility, fitting T(1)/T(2) ratios tends to underestimate the anisotropy of overall tumbling. An additional problem exists when the N-H bond vector directions are not distributed homogeneously over the surface of a unit sphere, such as in helix bundles or beta-sheets. Such a case was found in segment 4 of the gelation factor (ABP 120), an F-actin cross-linking protein, in which the diffusion tensor cannot be calculated from T(1)/T(2) ratios. The (15)N CSA tensor of the residues for this beta-sheet protein was found to vary even within secondary structure elements. The use of a common value for the whole protein molecule therefore might be an oversimplification. Using our approach it is immediately apparent that no exchange broadening exists for segment 4 although strongly reduced T(2) relaxation times for several residues could be mistaken as indications for exchange processes.     

Fine-tuning molecular acoustic models: sensitivity of the predicted attenuation to the Lennard-Jones parameters

In a previous paper [Y. Dain and R. M. Lueptow, J. Acoust. Soc. Am. 109, 1955 (2001)], a model of acoustic attenuation due to vibration-translation and vibration-vibration relaxation in multiple polyatomic gas mixtures was developed. In this paper, the model is improved by treating binary molecular collisions via fully pairwise vibrational transition probabilities. The sensitivity of the model to small variations in the Lennard-Jones parameters--collision diameter (sigma) and potential depth (epsilon)--is investigated for nitrogen-water-methane mixtures. For a N2(98.97%)-H2O(338 ppm)-CH4(1%) test mixture, the transition probabilities and acoustic absorption curves are much more sensitive to sigma than they are to epsilon. Additionally, when the 1% methane is replaced by nitrogen, the resulting mixture [N2(99.97%)-H2O(338 ppm)] becomes considerably more sensitive to changes of sigma(water). The current model minimizes the underprediction of the acoustic absorption peak magnitudes reported by S. G. Ejakov et al. [J. Acoust. Soc. Am. 113, 1871 (2003)].