R. de Beer

Java-based graphical user interface for the MRUI quantitation package.

This article describes the Java-based version of the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo MR spectroscopy data. We show that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI software. We have also established that MR quantitation algorithms, programmed in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI). This new graphical user interface (GUI) has been conceived for the processing of large data sets and uses prior knowledge data-bases to make interactive quantitation algorithms more userfriendly.

Retrieval of frequencies, amplitudes, damping factors, and phases from time-domain signals using a linear least-squares procedure

Abstract A new method for quantitative analysis of time-domain signals is reported. It amounts to fitting a function consisting of exponentially damped sinusoids with arbitrary phases to the data. By invoking the principle of linear prediction (LP) the fitting can be carried out by a linear least-squares (LS) procedure, and therefore needs no starting values The LS procedure is based on singular value decomposition (SVD), which enables one to distinguish between signal and noise. The method, denoted by LPSVD, yields a list comprising the frequency, damping factor, amplitude, and phase of each retrieved sinusoid. In addition, LPSVD is insensitive to truncation at the beginning and/or the end of the signal, and in fact is capable to accurately reconstruct the missing part. Preprocessing of the data is not necessary. Finally, the method achieves higher resolution than fast Fourier transformation.

SVD-based quantification of magnetic resonance signals

Abstract This study concerns the parametrization of NMR signals by state-space modeling (HSVD), which is based on singular value decomposition. It is shown that nonexponential decay can be parametrized by HSVD (and LPSVD). This property is applied to real-world NMR signals. In addition, we show that under certain conditions the computation time of SVD can be reduced very significantly. This is achieved by using the Lanczos algorithm and exploiting the Hankel structure of the data matrix. Proper orthogonalization of the singular vectors is realized.

Improved algorithm for noniterative time-domain model fitting to exponentially damped magnetic resonance signals

This communication is concerned with a new method of fitting a physical model function to a magnetic resonance signal, directly in the time domain. Our primary aim is analysis of the signal in quantitative terms, i.e., describing the signal in terms of physically meaningful parameters with their statistical errors. Before explaining the new method we make some remarks about the place of time-domain model fitting in spectral analysis. The notion of quantitative description just defined goes beyond constructing a spectrum from the available time-domain data. This judgment is supported by the observation that recently proposed methods for constructing a spectrum (l-3), although very useful for many purposes, have not provided values of the physical parameters involved. In fact, if the latter are wanted afterward, it is then still necessary to fit an appropriate model function to the spectrum (4, 5). Furthermore, in addition to the fitting, the degree to which the spectrum constructed approximates the “ideal” spectrum is to be assessed. On the basis of these considerations, we advocate the use of timedomain model fitting, if quantitative description of a signal is needed. On the other hand, if the primary need is to have a spectrum, one may well use methods such as proposed in Refs. (Z-3), some of which require significantly less computer time. If the signal decays exponentially, which is not uncommon in magnetic resonance, an additional advantage of remaining in the time domain emerges, namely that the fitting procedure can be made noniterative. To the best of our knowledge noniterative fitting procedures are not yet available for the frequency domain. A method of noniterative fitting has recently been devised by Kumaresan and Tufts (6) and was subsequently applied to magnetic resonance (7, 8) under the name LPSVD; see also (9) for a related method. An error analysis was given in (6, IO). We are here concerned with an alternative noniterative model fitting procedure, devised by Kung et al. (II) using the so-called state space formalism. The method can handle considerably more data points than LPSVD because polynomial rooting is avoided. At the same time, the residue of the fit is usually better than that of LPSVD. We shall indicate that the basic idea can be explained with elementary matrix algebra, without invoking the state space formalism. In addition, a formula for efficient computer implementation is given.

Analysis of NMR Data Using Time Domain Fitting Procedures

The beginning of this chapter sets out our main objective and how we intend to achieve it. As the title indicates, the content is concerned with parameter estimation in the time domain. Literally this is correct, but the term Time Domain is to be interpreted as Measurement Domain. Since in-vivo NMR measurements take place in the time domain, these two terms imply the same thing in practice. However, the intended interpretation should be kept in mind.

The prosthetic group of methylamine dehydrogenase from Pseudomonas AM1: Evidence for a quinone structure

The g-value and linewidth of ESR spectra of methylamine dehydrogenase (primary-amine:(acceptor) oxidoreductase (deaminating) EC 1.4.99.-) and methanol dehydrogenase (alcohol:(acceptor) oxidoreductase, EC 1.1.99.8) are very similar. This similarity is also reflected in electron-nuclear double resonance (ENDOR) results, the coupling constants of two protons in one enzyme equalling those in the other. The presence of a third proton in the ENDOR spectrum of methylamine dehydrogenase suggests a different structure or a different kind of interaction which can be related to the finding that the resolved ROSTHETIC GROUP IS PROTEIN-BOUND. The bound prosthetic group has a high redox-potential, supporting the conclusion from the ESR and ENDOR results that it is a quinone derivative.

Complete determination of 14N hyperfine and quadrupole interactions in the metastable triplet state of free‐base porphin via electron spin echo envelope modulation

Through the use of the electron spin echo envelope modulation method, we have accomplished the complete determination of the 14N hyperfine and quadrupole interaction tensors in the lowest photo‐excited triplet state of free‐base porphin in an n‐octane single crystal at ∼1.4 K. The results give insight into the molecular structure of the porphin in the excited state, the relationship between the nitrogen spin density and observed hyperfine couplings, and the effect of hydrogen bonding interactions on the quadrupole coupling constants and principal axes.

Measurement of hyperfine interactions with electron spin-echo spectroscopy. Application to F centers in KCl

Abstract The accuracy of spin-Hamiltonian determination via analysis of electron spin-echo nuclear modulation signals is investigated for F centers in KCl. It turns out that the accuracy matches that of ENDOR. The linewidth of the signals converted to the frequency domain also compares well with ENDOR. Parametric spectrum estimation with autoregressive modeling (maximum entropy method) yields significant further reduction of the linewidth. Analysis of the signal strength in the frequency domain appears feasible.

An electron spin‐echo envelope modulation study of the lowest triplet state of pyridine‐d5: Spin‐density distribution and structure

Recently we have shown that the lowest triplet state (T0) of pyridine, incorporated in a single crystal of benzene, may be studied by electron spin‐echo (ESE) spectroscopy. From the nitrogen hyperfine structure in the ESE detected electron paramagnetic resonance (EPR) spectra, we were able to conclude that pyridine, a planar molecule in the ground state, becomes nonplanar upon excitation into T0. Here we report the results of a detailed investigation of this distortion and of the electronic nature of the lowest triplet state of pyridine‐d5. We have performed electron spin–echo envelope modulation (ESEEM) spectroscopy. From the modulation spectra, the electron‐nuclear double resonance (ENDOR) frequencies corresponding to the various deuterium nuclei are obtained. Analysis of the dependence of these frequencies on the orientation of the magnetic field with respect to the triplet fine‐structure axes system allows for a determination of the deuterium hyperfine and quadrupole tensors. From these tensors and th...

ESR and ENDOR at 9 and 35 GHz on a powder of the enzyme methanol dehydrogenase from Hyphomicrobium X

ESR and ENDOR at 9 and 35 GHz have been applied to a powder of the enzyme methanol dehydrogenase from Hyphomicrobium X. The observed g‐tensor and ESR linewidth suggest that the protein‐bonded free radical originates from a quinone. ENDOR measurements at 35 GHz show that there are two strongly coupled protons in the free radical. The ENDOR response of the proton with the largest hyperfine coupling has been simulated by means of a line shape model. From this simulation the principal values of the hyperfine tensor could be extracted. The derived values indicate that the proton concerned is attached directly to a carbon of the quinoid ring.