MAG-PGSTE: a new STE-based PGSE NMR sequence for the determination of diffusion in magnetically inhomogeneous samples

A new stimulated echo based pulsed gradient spin-echo sequence, MAG-PGSTE, has been developed for the determination of self-diffusion in magnetically inhomogeneous samples. The sequence was tested on two glass bead samples (i.e., 212-300 and <106 microm glass bead packs). The MAG-PGSTE sequence was compared to the MAGSTE (or MPFG) (P.Z. Sun, J.G. Seland, D. Cory, Background gradient suppression in pulsed gradient stimulated echo measurements, J. Magn. Reson. 161 (2003) 168-173; P.Z. Sun, S.A. Smith, J. Zhou, Analysis of the magic asymmetric gradient stimulated echo sequence with shaped gradients, J. Magn. Reson. 171 (2004) 324-329; P.Z. Sun, Improved diffusion measurement in heterogeneous systems using the magic asymmetric gradient stimulated echo (MAGSTE) technique, J. Magn. Reson. 187 (2007) 177-183; P. Galvosas, F. Stallmach, J. K?rger, Background gradient suppression in stimulated echo NMR diffusion studies using magic pulsed field gradient ratios, J. Magn. Reson. 166 (2004) 164-173, P. Galvosas, PFG NMR-Diffusionsuntersuchungen mit ultra-hohen gepulsten magnetischen Feldgradienten an mikropor?sen Materialien, Ph.D. Thesis, Universit?t Leipzig, 2003, P.Z. Sun, Nuclear Magnetic Resonance Microscopy and Diffusion, Ph.D. Thesis, Massachusetts Institute of Technology, 2003] sequence and Cotts 13-interval [R.M. Cotts, M.J.R. Hoch, T. Sun, J.T. Marker, Pulsed field gradient stimulated echo methods for improved NMR diffusion measurements in heterogeneous systems, J. Magn. Reson. 83 (1989) 252-266] sequence using both glass bead samples. The MAG-PGSTE and MAGSTE (or MPFG) sequences outperformed the Cotts 13-interval sequence in the measurement of diffusion coefficients; more interestingly, for the sample with higher background gradients (i.e., the <106 microm glass bead sample), the MAG-PGSTE sequence provided higher signal-to-noise ratios and thus better diffusion measurements than the MAGSTE and Cotts 13-interval sequences. In addition, the MAG-PGSTE sequence provided good characterization of the surface-to-volume ratio for the glass bead samples.     

Conformational Equilibria in Polypeptides. II. Dihedral-Angle Distribution in Antamanide Based on Three-Bond Coupling Information

The use of³Jcoupling information in deriving dihedral-angle restraints for polypeptide-structure determination in the presence of conformational equilibria is illustrated withantamanide,cyclo(–Val¹–Pro²– Pro³– Ala⁴– Phe⁵– Phe⁶– Pro⁷– Pro⁸– Phe⁹– Phe¹⁰–). The experimental basis comprises accurate three-bond coupling constants as obtained from both homonuclear [C. Griesinger, O. W. Sørensen, and R. R. Ernst,J. Magn. Reson.75,474 (1987)] and heteronuclear [J. M. Schmidt,J. Magn. Reson.124,298 (1997)] exclusive correlation spectroscopy (E.COSY). For the backbone and side-chain dihedral angles in the nonproline residues, φ and χ₁, respectively, probability-distribution functions are derived and evaluated on the basis of χ²statistics and significance estimates. Various motional models are considered in the quantitative compilation of molecular-geometry parameters from spin-system parameters. From the³Jcoupling analysis, antamanide is found to possess a very flexible structure which is consistent with the results previously obtained in homonuclear NOE and¹³C–T₁relaxation studies. To fully agree with experiment, rotamer equilibria must be assumed for almost all of the torsions investigated in the peptide.     

Suppression of artifacts induced by homonuclear decoupling in amino-acid-type edited methyl H–C correlation experiments

A detailed theoretical and experimental analysis of the artifacts induced by homonuclear band-selective decoupling during CT frequency labeling is presented. The effects are discussed in the context of an amino-acid-type editing filter implemented in ¹H–¹³C CT-HSQC experiments of methyl groups in proteins. It is shown that both Bloch–Siegert shifts and modulation sidebands are efficiently suppressed by using additional off-resonance decoupling as proposed by Zhang and Gorenstein [J. Magn. Reson. 132 (1998) 81], and appropriate adjustment of a set of pulse sequence parameters. The theoretical predictions are confirmed by experiments performed on ¹³C-labeled protein samples, yielding artifact-free amino-acid-type edited methyl spectra.     

A mixed basis approach in the SGP-limit

A perturbation method for computing quick estimates of the echo decay in pulsed spin echo gradient NMR diffusion experiments in the short gradient pulse limit is presented. The perturbation basis involves (relatively few) dipole distributions on the boundaries generating a small perturbation matrix in O(s²) time, where s denotes the number of boundary elements. Several approximate eigenvalues and eigenfunctions to the diffusion operator are retrieved. The method is applied to 1D and 2D systems with Neumann boundary conditions.     

Removal of J-coupling peak distortion in PGSE experiments

Peak distortion caused by homonuclear J-coupling is a major problem that limits the utility of the pulsed-field gradient spin–echo (PGSE) method for studying translational diffusion. This unwanted effect can be removed by incorporation of anti-phase magnetization purging pulse elements at the end of the spin–echo sequence. Three methods, namely, trim-pulse, homospoil pulse gradient and chirp based z-filter were evaluated as potential candidates for an improved NMR diffusion method that is less sensitive to J-coupling peak distortion. The chirp based z-filter was found to be excellent in suppressing anti-phase magnetization while leaving the in-phase magnetization basically intact in spin–echo and stimulated-echo based experiments. The incorporation of chirp based z-filter into PGSE could allow diffusion analysis that would otherwise be impossible by conventional means.     

The effect of the diffusion time and pulse gradient duration ratio on the diffraction pattern and the structural information estimated from q-space diffusion MR: experiments and simulations

q-Space diffusion MRI (QSI) provides a means of obtaining microstructural information about porous materials and neuronal tissues from diffusion data. However, the accuracy of this structural information depends on experimental parameters used to collect the MR data. q-Space diffusion MR performed on clinical scanners is generally collected with relatively long diffusion gradient pulses, in which the gradient pulse duration, δ, is comparable to the diffusion time, Δ. In this study, we used phantoms, consisting of ensembles of microtubes, and mathematical models to assess the effect of the ratio of the diffusion time and the duration of the diffusion pulse gradient, i.e., Δ/δ, on the MR signal attenuation vs. q, and on the measured structural information extracted therefrom. We found that for Δ/δ  1, the diffraction pattern obtained from q-space MR data are shallower than when the short gradient pulse (SGP) approximation is satisfied. For long δ the estimated compartment size is, as expected, smaller than the real size. Interestingly, for Δ/δ  1 the diffraction peaks are shifted to even higher q-values, even when δ is kept constant, giving the impression that the restricted compartments are even smaller than they are. When phantoms composed of microtubes of different diameters are used, it is more difficult to estimate the diameter distribution in this regime. Excellent agreement is found between the experimental results and simulations that explicitly account for the use of long duration gradient pulses. Using such experimental data and this mathematical framework, one can estimate the true compartment dimensions when long and finite gradient pulses are used even when Δ/δ  1.     

A Pulsed Field Gradient Spin-Echo Method for Diffusion Measurements in the Presence of Internal Gradients

Over the past decade several pulsed field gradient stimulated-echo methods have been presented for diffusion measurements in heterogeneous media. These methods have reduced or eliminated the coupling between the applied magnetic field gradient and a constant internal magnetic field gradient caused by susceptibility changes throughout the sample. For many research purposes thez-storage delay between the second and third π/2 RF pulse has been included in order to increase the decay of the echo attenuation to an appropriate level and to increase the signal-to-noise ratio by avoidingT₂relaxation of the magnetization in parts of the pulse sequence. For these reasons a stimulated-echo method has been applied instead of a spin-echo method. When studying systems where it is necessary to keep the duration of the pulse sequence at a minimum, and one is not dependent on usingz-storage time to increase the echo attenuation or to study diffusion as a function of observation time, a spin-echo method should be chosen. Here we propose a bipolar pulsed field gradient spin-echo method which is well suited to this purpose, and preliminary diffusion measurements are presented as illustration.     

The AΠu state of : Electric properties, fine and hyperfine coupling constants, and magnetic moments (g-factors). A theoretical study

Several properties are calculated for A²Π_u of —the majority for the first time—including electric and magnetic moments, and fine/hyperfine structure (fs/hfs) parameters. The new results are compared with our previous ones for X² and B² of [P.J. Bruna, F. Grein, J. Mol. Spectrosc. 227 (2004) 67–80]. The electric quadrupole Θ and hexadecapole Φ moments, polarizability α, and hfs constants a, b, c, d, eQq₀, eQq₂ are evaluated at the density functional theory (DFT) level [B3LYP/aug-cc-pVQZ]. The fs constants (spin–orbit coupling A_Π, Λ-doubling p, q, spin-rotation γ_Π), and magnetic moments (g-factors) are obtained via 2nd-order sum-over-states expansions, using wavefunctions and matrix elements obtained with a multireference configuration interaction (MRDCI) method, and the Breit–Pauli Hamiltonian. At equilibrium, 2nd-order properties of A²Π_u are dominated by its coupling with B². For the A state, two independent components are reported for traceless tensor properties (multipoles Θ and Φ; hfs parameters c/d and q₀/q₂) and three for traced properties (polarizability α and g-factors), i.e., one more component than for axially symmetric Σ states. The currently available experimental data on — limited to A_Π, p, and q—are well reproduced by our theoretical results.     

Double-quantum filtration under rotational-resonance conditions: numerical simulations and experimental results

The dependence of the performance of a recently introduced pulse sequence to achieve double-quantum excitation under the n = 1 rotational-resonance condition (T. Karlsson, M. Edén, H. Luthman, and M. H. Levitt, 2000, J. Magn. Reson. 145, 95–107) on different spin-system properties is investigated by means of numerical simulations and ¹³C MAS NMR experiments. For spin systems where chemical shielding anisotropies amount to only an insignificant fraction of the isotropic chemical shielding difference, high efficiencies are found for large and small dipolar coupling interactions. In the presence of significant chemical shielding anisotropies the overall efficiencies decrease and become strongly dependent on the duration of the excitation period. It is demonstrated that those spin-system parameters which are sensitively encoded in the lineshapes of a conventional n = 1 rotational-resonance spectrum are similarly sensitively encoded in the corresponding rotational-resonance double-quantum-filtered lineshapes and may be quantitatively recovered by iterative lineshape-fitting approaches. In certain favorable circumstances, the in-built selectivity of the rotational-resonance double-quantum-filtration approach permits successful application of the experiment on spin systems with more than two spins.     

The Multidimensional Filter Diagonalization Method: II. Application to 2D Projections of 2D, 3D, and 4D NMR Experiments

The theory of the multidimensional filter diagonalization method (FDM) described in the previous paper (V. A. Mandelshtam, 2000, J. Magn. Reson. 144, 343–356 (2000)) is applied to NMR time signals with up to four independent time variables. Direct projections of the multidimensional time signals produce new kinds of 2D spectra. The resolution obtained by FDM can be far superior to that obtained by conventional phase-sensitive FT processing, and correlation peaks in heteronuclear and homonuclear experiments can be condensed to sharp singlets, removing all spin–spin couplings. Examples of singlet-HSQC and singlet-TOCSY spectra show big gains in resolution. It is not necessary to have a finely digitized spectrum, in which the individual multiplet components are resolved, for the methods to work. Examples of FDM spectra, ranging from simple organic molecules and steroids to metalloproteins, are shown.     

Signal Enhancement Using 45° Water Flipback for 3D N-Edited ROESY and NOESY HMQC and HSQC

A novel implementation of the water flipback technique employing a 45° flip-angle water-selective pulse is presented. The use of this water flipback technique is shown to significantly enhance signal in 3D ¹⁵N-edited ROESY in a 20 kDa complex of the vnd/NK-2 homeodomain bound to DNA. The enhancement is seen relative to the same experiment using weak water presaturation during the recovery delay. This enhancement is observed for the signals from both labile and nonlabile protons. ROESY and NOESY pulse sequences with 45° water flipback are presented using both HMQC and HSQC for the ¹⁵N dimension. The 45° flipback pulse is followed by a gradient, a water selective 180° pulse, and another gradient to remove quadrature images and crosspeak phase distortion near the water frequency. Radiation damping of the water magnetization during the t₁ and t₂ evolution periods is suppressed using gradients. Water resonance planes from NOESY–HMQC and NOESY–HSQC spectra show that the HMQC version of the pulse sequences can provide stronger signal for very fast exchanging protons. The HSQC versions of the ROESY and NOESY pulse sequences are designed for the quantitative determination of protein–water crossrelaxation rates, with no water-selective pulses during the mixing time and with phase cycling and other measures for reducing axial artifacts in the water signal.     

Matrix pseudogroups associated with anti-commutative plane

A C ^*-formulation of quantum 2×2 matrix groups for the deformation parameter q=–1 is given.     

One- and two-dimensional C–H/N–H dipolar correlation experiments under fast magic-angle spinning for determining the peptide dihedral angle φ

A recently proposed ¹³C–¹H recoupling sequence operative under fast magic-angle spinning (MAS) [K. Takegoshi, T. Terao, Solid State Nucl. Magn. Reson. 13 (1999) 203–212.] is applied to observe ¹³C–¹H and ¹⁵N–¹H dipolar powder patterns in the ¹H–¹⁵N–¹³C–¹H system of a peptide bond. Both patterns are correlated by ¹⁵N-to-¹³C cross polarization to observe one- or two-dimensional (1D or 2D) correlation spectra, which can be simulated by using a simple analytical expression to determine the H–N–C–H dihedral angle. The 1D and 2D experiments were applied to N-acetyl[1,2-¹³C,¹⁵N] -valine, and the peptide φ angle was determined with high precision by the 2D experiment to be ±155.0°±1.2°. The positive one is in good agreement with the X-ray value of 154°±5°. The 1D experiment provided the value of φ=±156.0°±0.8°.     

Correlation inequalities and the Kosterlitz-Thouless transition for anisotropic rotators

I give a proof of the Kosterlitz-Thouless transition for sufficiently anisotropic (J _zJ _x ^–1 =J _zJ _y ^–1 <2q ^–(JKT)^–J) two-dimensionalN-component rotators (N 3). The method is based on Wells' inequality and is related to mean field Gaussian inequalities.     

Accurate Measurements of Multiple-Bond C–H Coupling Constants from Phase-Sensitive 2D INEPT Spectra

Measurements of multiple-bond ¹³C–¹H coupling constants are of great interest for the assignment of nonprotonated ¹³C resonances and the elucidation of molecular conformation in solution. Usually, the heteronuclear multiple-bond coupling constants were measured either by the J_CH splittings mostly in selective 2D spectra or in 3D spectra, which are time consuming, or by the cross peak intensity analysis in 2D quantitative heteronuclear J correlation spectra (1994, G. Zhu, A. Renwick, and A. Bax, J. Magn. Reson. A 110, 257; 1994, A. Bax, G. W. Vuister, S. Grzesiek, F. Delaglio, A. C. Wang, R. Tschudin, and G. Zhu, Methods Enzymol. 239, 79.), which suffer from the accuracy problem caused by the signal-to-noise ratio and the nonpure absorptive peak patterns. Concerted incrementation of the duration for developing proton antiphase magnetization with respect to carbon-13 and the evolution time for proton chemical shift in different steps in a modified INEPT pulse sequence provides a new method for accurate measurements of heteronuclear multiple-bond coupling constants in a single 2D experiment.     

The accuracy of whole brain N-acetylaspartate quantification

A non-localizing pulse sequence to quantify the total amount of N-acetylaspartate (NAA) in the whole brain (WBNAA) was introduced recently [Magn. Reson. Med. 40, 684–689 (1998)]. However, it is known that regional magnetic field inhomogeneities, ΔB₀s, arising from susceptibility differences at tissue interfaces, shift and broaden local resonances to outside the integration window, leading to an underestimation of the true amount of NAA in the entire brain. To quantify the upper limit of this loss, the whole-head proton MR spectrum (¹H-MRS) of the water was integrated over the same frequency width as the NAA. The ratio of this area/total-water-line was 75 ± 5% in 5 volunteers. The procedure was repeated with the brain-only water peak, obtained by summing signals only from voxels within that organ from a three-dimensional chemical-shift-imaging (3D CSI) set. It indicated that <10% of the water signal loss occurred in the brain. Therefore, by analogy, WBNAA accounts for >90% of that metabolite.     

Effects of finite-width pulses in the pulsed-field gradient measurement of the diffusion coefficient in connected porous media

We analytically compute the apparent diffusion coefficient D(app) for an open restricted geometry, such as an extended porous medium, for the case of a pulsed-field gradient (PFG) experiment with finite-width pulses. In the short- and long-time limits, we give explicit, model-independent expressions that correct for the finite duration of the pulses and can be used to extract the pore surface-to-volume (S/V) ratio as well as the tortuosity. For all times, we compute D(app) using a well-established model form of the actual time-dependent diffusion coefficient D(t) that can be obtained from an ideal narrow-pulse PFG. We compare D(app) and D(t) and find that, regardless of pulse widths and geometry-dependent parameters, the two quantities deviate by less than 20%. These results are in sharp contrast with the studies on closed geometries [J. Magn. Reson. A 117 (1995) 209], where the effects of finite gradient-pulse widths are large. The analytical results presented here can be easily adapted for different pulse protocols and time sequences.     

MQ-PGSTE: A new multi-quantum STE-based PGSE NMR sequence

A new multi-quantum stimulated echo based pulsed gradient spin-echo sequence, MQ-PGSTE, has been developed for measuring translational diffusion. The new sequence provides a higher signal-to-noise ratio than the (Hahn spin-echo based) MAXY-D sequence at long diffusion times, and thus potentially affords better diffusion measurements on macromolecule samples. Based on multi-quantum coherence encoding, the MQ-PGSTE sequence needs considerably lower gradient strengths for diffusion characterization compared to standard single quantum pulsed gradient spin-echo sequences. By using the new sequence, the diffusion coefficient of l-[3-¹³C]-alanine was found to be 8.1 ± 0.1 × 10⁻¹⁰ m² s⁻¹, which is in line with the value obtained by the use of the standard stimulated echo based pulsed gradient spin-echo sequence.     

Structural analysis of uniformly C-labelled solids from selective angle measurements at rotational resonance

We demonstrate that individual H–C–C–H torsional angles in uniformly labelled organic solids can be estimated by selective excitation of ¹³C double-quantum coherences under magic-angle spinning at rotational resonance. By adapting a straightforward one-dimensional experiment described earlier [T. Karlsson, M. Eden, H. Luhman, M.H. Levitt, J. Magn. Reson. 145 (2000) 95–107], a double-quantum filtered spectrum selective for Cα and Cβ of uniformly labelled l-[¹³C,¹⁵N]valine is obtained with 25% efficiency. The evolution of Cα–Cβ double-quantum coherence under the influence of the dipolar fields of bonded protons is monitored to provide a value of the Hα–Cα–Cβ–Hβ torsional angle that is consistent with the crystal structure. In addition, double-quantum filtration selective for C6 and C1′ of uniformly labelled [¹³C,¹⁵N]uridine is achieved with 12% efficiency for a ¹³C–¹³C distance of 2.5 Å, yielding a reliable estimate of the C6–H and C1′–H projection angle defining the relative orientations of the nucleoside pyrimidine and ribose rings. This procedure will be useful, in favourable cases, for structural analysis of fully labelled small molecules such as receptor ligands that are not readily synthesised with labels placed selectively at structurally diagnostic sites.