Improved Spin-Echo-Edited NMR Diffusion Measurements

The need for simple and robust schemes for the analysis of ligand-protein binding has resulted in the development of diffusion-based NMR techniques that can be used to assay binding in protein solutions containing a mixture of several ligands. As a means of gaining spectral selectivity in NMR diffusion measurements, a simple experiment, the gradient modified spin-echo (GOSE), has been developed to reject the resonances of coupled spins and detect only the singlets in the (1)H NMR spectrum. This is accomplished by first using a spin echo to null the resonances of the coupled spins. Following the spin echo, the singlet magnetization is flipped out of the transverse plane and a dephasing gradient is applied to reduce the spectral artifacts resulting from incomplete cancellation of the J-coupled resonances. The resulting modular sequence is combined here with the BPPSTE pulse sequence; however, it could be easily incorporated into any pulse sequence where additional spectral selectivity is desired. Results obtained with the GOSE-BPPSTE pulse sequence are compared with those obtained with the BPPSTE and CPMG-BPPSTE experiments for a mixture containing the ligands resorcinol and tryptophan in a solution of human serum albumin.     

A Finite Volume Method for the Approximation of Diffusion Operators on Distorted Meshes

A new finite volume method is presented for discretizing general linear or nonlinear elliptic second-order partial-differential equations with mixed boundary conditions. The advantage of this method is that arbitrary distorted meshes can be used without the numerical results being altered. The resulting algorithm has more unknowns than standard methods like finite difference or finite element methods. However, the matrices that need to be inverted are positive definite, so the most powerful linear solvers can be applied. The method has been tested on a few elliptic and parabolic equations, either linear, as in the case of the standard heat diffusion equation, or nonlinear, as in the case of the radiation diffusion equation and the resistive diffusion equation with Hall term.     

NMR Relaxation and Diffusion Measurements on Iron(III)-Doped Kaolin Clay

Kaolin clay samples were mixed with various amounts of Fe₂O₃ powder. The influence of this magnetic impurity on NMR relaxation and diffusion measurements on the water in this porous material was investigated. The NMR relaxation measurements showed a nearly mono-exponential decay, leading to the conclusion that the pore size distribution of the clay samples is either narrow and/or that the pores are interconnected very well. Both the longitudinal and the transverse relaxation rate depend linearly on the concentration of the Fe₂O₃ impurity. The NMR diffusion measurements revealed that the Fe₂O₃ causes internal magnetic field gradients that largely exceed the maximum external gradient that could be applied by our NMR apparatus (0.3 T/m). Additional SQUID measurements yielded the magnetization and magnetic susceptibility of the samples at the magnetic field strength used in the NMR measurements (0.8 T). A theoretical estimate of the internal magnetic field gradients leads to the conclusion that the water in the porous clay samples cannot be described by the commonly observed motional averaging regime. Probably an intermediate or a localization regime is induced by the large internal gradients, which are estimated to be on the order of 1 to 10 T/m in the pore volume and may exceed 1000 T/m at the pore surface.     

A new time-domain frequency-selective quantification algorithm

In this paper a new time-domain frequency-selective quantification algorithm is presented. Frequency-selective quantification refers to a method that analyzes spectral components in a selected frequency region, ignoring all the other components outside. The algorithm, referred to as MeFreS (Metropolis Frequency-Selective), is based on rank minimization of an opportune Hankel matrix. The minimization procedure is satisfied by the down-hill simplex method, implemented with the simulated annealing method. MeFreS does not use any preprocessing step or filter to suppress nuisance peaks, but the signal model function is directly fitted. In this manner, neither inherent signal distortions nor estimation biases to be corrected occur. The algorithm was tested with Monte Carlo simulations. A comparison with VARPRO and AMARESw algorithms was carried out. Finally, two samples of known content from NMR data were quantified.     

2D(13)C-(13)C MAS NMR correlation spectroscopy with mixing by true (1)H spin diffusion reveals long-range intermolecular distance restraints in ultra high magnetic field

An improved 2D (13)C-(13)C CP(3) MAS NMR correlation experiment with mixing by true (1)H spin diffusion is presented. With CP(3), correlations can be detected over a much longer range than with direct (1)H-(13)C or (13)C-(13)C dipolar recoupling. The experiment employs a (1)H spin diffusion mixing period tau(m) sandwiched between two cross-polarization periods. An optimized CP(3) sequence for measuring polarization transfer on a length scale between 0.3 and 1.0 nm using short mixing times of 0.1 ms < tau(m) < 1 ms is presented. For such a short tau(m), cross talk from residual transverse magnetization of the donating nuclear species after a CP can be suppressed by extended phase cycling. The utility of the experiment for genuine structure determination is demonstrated using a self-aggregated Chl a/H(2)O sample. The number of intramolecular cross-peaks increases for longer mixing times and this obscures the intermolecular transfer events. Hence, the experiment will be useful for short mixing times only. For a short tau(m) = 0.1 ms, intermolecular correlations are detected between the ends of phytyl tails and ring carbons of neighboring Chl a molecules in the aggregate. In this way the model for the structure, with stacks of Chl a that are arranged back to back with interdigitating phytyl chains stretched between two bilayers, is validated.     

Solid-state NMR spectroscopy of paramagnetic metallocenes

The paramagnetic metallocenes and decamethylmetallocenes (C(5)H(5))(2)M and (C(5)Me(5))(2)M with M=V (S=3/2), Mn (S=5/2 or 1/2), Co (S=1/2), and Ni (S=1) were studied by (1)H and (13)C solid-state MAS NMR spectroscopy. Near room temperature spinning sideband manifolds cover ranges of up to 1100 and 3500 ppm, and isotropic signal shifts appear between -260 and 300 ppm and between -600 and 1640 ppm for (1)H and (13)C NMR spectra, respectively. The isotropic paramagnetic signal shifts, which are related to the spin densities in the s orbital of ligand atoms, were discussed. A Herzfeld--Berger spinning sideband analysis of the ring carbon signals yielded the principal values of the paramagnetic shift tensors, and for metallocenes with a small g-factor anisotropy the electron spin density in the ligand pi system was determined from the chemical shift anisotropy. The unusual features of the (1)H and (13)C solid-state NMR spectra of manganocene were related to its chain structure while temperature-dependent (1)H MAS NMR studies reflected antiferromagnetic interaction between the spin centers.     

Application of high-resolution magic-angle spinning NMR spectroscopy to define the cell uptake of MRI contrast agents

A new method, based on proton high-resolution magic-angle spinning ((1)H HR-MAS) NMR spectroscopy, has been employed to study the cell uptake of magnetic resonance imaging contrast agents (MRI-CAs). The method was tested on human red blood cells (HRBC) and white blood cells (HWBC) by using three gadolinium complexes, widely used in diagnostics, Gd-BOPTA, Gd-DTPA, and Gd-DOTA, and the analogous complexes obtained by replacing Gd(III) with Dy(III), Nd(III), and Tb(III) (i.e., complexes isostructural to the ones of gadolinium but acting as shift agents). The method is based on the evaluation of the magnetic effects, line broadening, or induced lanthanide shift (LIS) caused by these complexes on NMR signals of intra- and extracellular water. Since magnetic effects are directly linked to permeability, this method is direct. In all the tests, these magnetic effects were detected for the extracellular water signal only, providing a direct proof that these complexes are not able to cross the cell membrane. Line broadening effects (i.e., the use of gadolinium complexes) only allow qualitative evaluations. On the contrary, LIS effects can be measured with high precision and they can be related to the concentration of the paramagnetic species in the cellular compartments. This is possible because the HR-MAS technique provides the complete elimination of bulk magnetic susceptibility (BMS) shift and the differentiation of extra- and intracellular water signals. Thus with this method, the rapid quantification of the MRI-CA amount inside and outside the cells is actually feasible.     

Probing Proteins in Solution by Xe NMR Spectroscopy

The interaction of xenon with different proteins in aqueous solution is investigated by ¹²⁹Xe NMR spectroscopy. Chemical shifts are measured in horse metmyoglobin, hen egg white lysozyme, and horse cytochrome c solutions as a function of xenon concentration. In these systems, xenon is in fast exchange between all possible environments. The results suggest that nonspecific interactions exist between xenon and the protein exteriors and the data are analyzed in term of parameters which characterize the protein surfaces. The experimental data for horse metmyoglobin are interpreted using a model in which xenon forms a 1:1 complex with the protein and the chemical shift of the complexed xenon is reported (Locci et al., Keystone Symposia “Frontiers of NMR in Molecular Biology VI”, Jan. 9–15, 1999, Breckenridge, CO, Abstract E216, p. 53; Locci et al., XeMAT 2000 “Optical Polarization and Xenon NMR of Materials”, June 28–30, 2000, Sestri Levante, Italy, p. 46).     

GAMMA simulations of stray field responses: slice thickness and pulse calibration

A stray field (STRAFI) module has been added to the GAMMA magnetic resonance simulation platform in order to facilitate computational investigations of NMR experiments in large static field gradients that are on the order of 50 T/m. The package has been used to examine system response during echo trains generated by the application of shaped pulses. The associated echo amplitude maxima and effective slice thickness are presented. A new accurate method for STRAFI pulse calibration based on relative echo amplitudes is proposed.     

Generation and Application of Ultra-High-Intensity Magnetic Field Gradient Pulses for NMR Spectroscopy

Two different concepts of gradient current power supplies are introduced, which are suitable for the generation of ultra-high intensity pulsed magnetic field gradients of alternating polarity. The first system consists of a directly binary coded current source (DBCCS). It yields current pulses of up to ±120 A and a maximum voltage across the gradient coil of ±400 V. The second system consists of two TECHRON 8606 power supplies in push–pull configuration (PSPPC). It yields current pulses of up to ±100 A and a maximum voltage across the gradient coil of ±300 V. In combination with actively shielded anti-Helmholtz gradient coils, both systems are used routinely in NMR diffusion studies with unipolar pulsed field gradients of up to 35 T/m. Until now, alternating pulsed field gradient experiments were successfully performed with gradient intensities of up to ±25 T/m (DBCCS) and ±35 T/m (PSPPC), respectively. Based on the observation of the NMR spin echo in the presence of a small read gradient, procedures to test the stability and the matching of such ultra-high pulsed field gradient intensities as well as an automated routine for the compensation of possible mismatches are introduced. The results of these procedures are reported for the PSPPC system.     

One micrometer resolution NMR microscopy

We obtained a magnetic resonance image of 1 microm resolution and 75 microm(3) voxel volume for a phantom filled with hydrocarbon oil within an hour at 14.1 T. For this work, a specially designed probe with a high sensitivity RF coil and gradient coils generating over 1000 G/cm was built. The optimal pulse sequence was analyzed in consideration of the bandwidth, diffusion coefficients, and T(1) and T(2) relaxations of the medium. The system was applied to the in vivo imaging of a geranium leaf stem to get the images of 2 microm resolution and 200 microm(3) voxel volume.     

Solution of Time-Dependent Diffusion Equations with Variable Coefficients Using Multiwavelets

A new numerical algorithm is developed for the solution of time-dependent differential equations of diffusion type. It allows for an accurate and efficient treatment of multidimensional problems with variable coefficients, nonlinearities, and general boundary conditions. For space discretization we use the multiwavelet bases introduced by Alpert (1993,SIAM J. Math. Anal.24, 246–262), and then applied to the representation of differential operators and functions of operators presented by Alpert, Beylkin, and Vozovoi (Representation of operators in the multiwavelet basis, in preparation). An important advantage of multiwavelet basis functions is the fact that they are supported only on non-overlapping subdomains. Thus multiwavelet bases are attractive for solving problems in finite (non periodic) domains. Boundary conditions are imposed with a penalty technique of Hesthaven and Gottlieb (1996,SIAM J. Sci. Comput., 579–612) which can be used to impose rather general boundary conditions. The penalty approach was extended to a procedure for ensuring the continuity of the solution and its first derivative across interior boundaries between neighboring subdomains while time stepping the solution of a time dependent problem. This penalty procedure on the interfaces allows for a simplification and sparsification of the representation of differential operators by discarding the elements responsible for interactions between neighboring subdomains. Consequently the matrices representing the differential operators (on the finest scale) have block-diagonal structure. For a fixed order of multiwavelets (i.e., a fixed number of vanishing moments) the computational complexity of the present algorithm is proportional to the number of subdomains. The time discretization method of Beylkin, Keiser, and Vozovoi (1998, PAM Report 347) is used in view of its favorable stability properties. Numerical results are presented for evolution equations with variable coefficients in one and two dimensions.     

Particle Transport through Scattering Regions with Clear Layers and Inclusions

This paper introduces generalized diffusion models for the transport of particles in scattering media with nonscattering inclusions. Classical diffusion is known as a good approximation of transport only in scattering media. Based on asymptotic expansions and the coupling of transport and diffusion models, generalized diffusion equations with nonlocal interface conditions are proposed which offer a computationally cheap, yet accurate, alternative to solving the full phase-space transport equations. The paper shows which computational model should be used depending on the size and shape of the nonscattering inclusions in the simplified setting of two space dimensions. An important application is the treatment of clear layers in near-infrared (NIR) spectroscopy, an imaging technique based on the propagation of NIR photons in human tissues.     

NMR spectral quantitation by principal component analysis. III. A generalized procedure for determination of lineshape variations

We present a general procedure for automatic quantitation of a series of spectral peaks based on principal component analysis (PCA). PCA has been previously used for spectral quantitation of a single resonant peak of constant shape but variable amplitude. Here we extend this procedure to estimate all of the peak parameters: amplitude, position (frequency), phase and linewidth. The procedure consists of a series of iterative steps in which the estimates of position and phase from one stage of iteration are used to correct the spectra prior to the next stage. The process is convergent to a stable result, typically in less than 5 iterations. If desired, remaining linewidth variations can then be corrected. Correction of (typically) unwanted variations of these types is important not only for direct peak quantitation, but also as a preprocessing step for spectral data prior to application of pattern recognition/classification techniques. The procedure is demonstrated on simulated data and on a set of 992 (31)P NMR in vivo spectra taken from a kinetic study of rat muscle energetics. The proposed procedure is robust, makes very limited assumptions about the lineshape, and performs well with data of low signal-to-noise ratio.     

A subspace time-domain algorithm for automated NMR spectral normalization

Recently, two methods have been proposed for quantitatively comparing NMR spectra of control and treated samples, in order to examine the possible occurring variations in cell metabolism and/or structure in response to numerous physical, chemical, and biological agents. These methods are the maximum superposition normalization algorithm (MaSNAl) and the minimum rank normalization algorithm (MiRaNAl). In this paper a new subspace-based time-domain normalization algorithm, denoted by SuTdNAl (subspace time-domain normalization algorithm), is presented. By the determination of the intersection of the column spaces of two Hankel matrices, the common signal poles and further on the components having proportionally varying amplitudes are detected. The method has the advantage that it is computationally less intensive than the MaSNAl and the MiRaNAl. Furthermore, no approximate estimate of the normalization factor is required. The algorithm was tested by Monte Carlo simulations on a set of simulation signals. It was shown that the SuTdNAl has a statistical performance similar to that of the MiRaNAl, which itself is an improvement over the MaSNAl. Furthermore, two samples of known contents are compared with the MiRaNAl, the SuTdNAl, and an older method using a standard. Finally, the SuTdNAl is tested on a realistic simulation example derived from an in vitro measurement on cells.     

Physics-Based Preconditioning and the Newton–Krylov Method for Non-equilibrium Radiation Diffusion

An algorithm is presented for the solution of the time dependent reaction-diffusion systems which arise in non-equilibrium radiation diffusion applications. This system of nonlinear equations is solved by coupling three numerical methods, Jacobian-free Newton–Krylov, operator splitting, and multigrid linear solvers. An inexact Newton's method is used to solve the system of nonlinear equations. Since building the Jacobian matrix for problems of interest can be challenging, we employ a Jacobian–free implementation of Newton's method, where the action of the Jacobian matrix on a vector is approximated by a first order Taylor series expansion. Preconditioned generalized minimal residual (PGMRES) is the Krylov method used to solve the linear systems that come from the iterations of Newton's method. The preconditioner in this solution method is constructed using a physics-based divide and conquer approach, often referred to as operator splitting. This solution procedure inverts the scalar elliptic systems that make up the preconditioner using simple multigrid methods. The preconditioner also addresses the strong coupling between equations with local 2×2 block solves. The intra-cell coupling is applied after the inter-cell coupling has already been addressed by the elliptic solves. Results are presented using this solution procedure that demonstrate its efficiency while incurring minimal memory requirements.     

Determination of membrane Peptide orientation by 1H-detected 2H NMR spectroscopy

We demonstrate the application of the proton inverse detected deuteron (PRIDE) NMR technique to the measurement of the orientation of membrane-bound peptides with enhanced sensitivity. Gramicidin D, a transmembrane peptide, and ovispirin, a surface-bound peptide, were used as model systems. The peptides were 2H-labeled by 1H/2H exchange and oriented uniaxially on glass plates. The directly detected 2H spectra of both peptides showed only a strong D(2)O signal and no large quadrupolar splittings. In contrast, the PRIDE spectrum of gramicidin exhibited quadrupolar splittings as large as 281 kHz, consistent with its transmembrane orientation. Moreover, the large D(2)O signal in the directly detected 2H spectra was cleanly suppressed in the PRIDE spectrum. For ovispirin, the 1H indirectly detected 2H spectrum revealed a 104 kHz splitting and a zero-frequency peak. The former reflects the in-plane orientation of most of the helix axis, while the latter results from residues with a magic-angle orientation of the N-D bonds. These are consistent with previous 15N NMR results on ovispirin. The combination of PRIDE and exchange labeling provides an economical and sensitive method of studying membrane peptide orientations in lipid bilayers without the influence of D(2)O and with the ability to detect N-D bonds at the magic angle from the bilayer normal.     

Convection compensated electrophoretic NMR

A novel method of convection compensated ENMR (CC-ENMR) has been developed to detect electrophoretic motion of ionic species in the presence of bulk solution convection. This was accomplished using a gradient moment nulling technique to remove spectral artifacts from heat-induced convection and using the polarity switch of the applied electric field to retain spin phase modulations due to electrophoretic flow. Experiments were carried out with a mixture of 100 mM L-aspartic acid and 100 mM 4,9-dioxa-1,12-dodecanediamine to demonstrate this new method of ENMR. CC-ENMR enhances our previously developed capillary array ENMR (CA-ENMR) in solving the convection problem. The combined CA- and CC-ENMR approach strengthens the potential of multidimensional ENMR in simultaneous structural determination of coexisting proteins and protein conformations in biological buffer solutions of high ionic strength. Structural mapping of interacting proteins during biochemical reactions becomes possible in the future using ENMR techniques, which may have a profound impact on the understanding of biological events, including protein folding, genetic control, and signal transduction in general.     

Wave Simulation in Frozen Porous Media

We propose a numerical algorithm for simulation of wave propagation in frozen porous media, where the pore space is filled with ice and water. The model, based on a Biot-type three-phase theory, predicts three compressional waves and two shear waves and models the attenuation level observed in rocks. Attenuation is modeled with exponential relaxation functions which allow a differential formulation based on memory variables. The wavefield is obtained using a grid method based on the Fourier differential operator and a Runge–Kutta time-integration algorithm. Since the presence of slow quasistatic modes makes the differential equations stiff, a time-splitting integration algorithm is used to solve the stiff part analytically. The modeling is second-order accurate in the time discretization and has spectral accuracy in the calculation of the spatial derivatives.     

A two-dimensional artifact from asynchronous decoupling

Many heteronuclear NMR experiments employ decoupling to collapse the heteronuclear multiplet, using decoupling schemes with a periodic phase modulation like WALTZ, MLEV, or GARP. Because of the periodic nature of these schemes, cycling sidebands are generated, whose intensity can be strongly reduced by decoupling asynchronously. We show that the most common implementation of asynchronous decoupling on modern spectrometers is such that the cycling sidebands are subjected to a periodic modulation. For multidimensional experiments, this results in ridges that can seriously compromise the quality of the spectrum. Based on our model, the artifact in a 2D [(1)H]-(15)N NOE equilibrium experiment is simulated and it is shown that the artifact can be prevented by using synchronous decoupling.