Biomedical subjects

A J Shaka

Publications and source records attributed to A J Shaka.

8 recordsLinked to original sources

PubMed1999

Composite pulsed field gradients with refocused chemical shifts and short recovery time.

An improved self-compensating pulsed field gradient (PFG) technique that combines antiphase gradient pairs with broadband frequency-modulated 180 degrees pulses is proposed. The antiphase gradient pairs lead to superb system recovery. In addition, evolution under chemical shift and heteronuclear J coupling are refocused during the PFG, making it appear effectively instantaneous. This new approach makes it possible to obtain high-resolution phase-sensitive 2D spectra for the PFG version of many experiments such as COSY, DQF-COSY, and HSQC without adding extra compensating delays or pulses. While reasonable suppression of unwanted magnetization is achieved, this method also gives satisfactory retention of desired signals. As a bonus, the field-frequency lock is not perturbed during the experiments.

Carbon↗

PubMed1999

Pure absorption electron spin echo envelope modulation spectra by using the filter-diagonalization method for harmonic inversion.

Harmonic inversion of electron spin echo envelope (ESEEM) time-domain signals by filter diagonalization is investigated as an alternative to Fourier transformation. It is demonstrated that this method features enhanced resolution compared to Fourier-transform magnitude spectra, since it can eliminate dispersive contributions to the line shape, even if no linear phase correction is possible. Furthermore, instrumental artifacts can be easily removed from the spectra if they are narrow either in time or frequency domain. This applies to echo crossings that are only incompletely eliminated by phase cycling and to spurious spectrometer frequencies, respectively. The method is computationally efficient and numerically stable and does not require extensive parameter adjustments or advance knowledge of the number of spectral lines. Experiments on gamma-irradiated methyl-alpha-d-glucopyranoside show that more information can be obtained from typical ESEEM time-domain signals by filter-diagonalization than by Fourier transformation.

Absorption↗

PubMed1999

Observation of long-range small-molecule NOEs using a neoteric sensitivity enhancement scheme.

A new method to increase the sensitivity of the 1D transient NOE experiment for molecules in the positive NOE regime is presented. This method, the reverse NOE, simply replaces the conventional relaxation delay between scans. Transient positive NOE enhancements from all other spins are used to accelerate the recovery of the target resonance toward its equilibrium intensity. In favorable cases, the intensity of the target peak at the start of an experiment can actually be increased beyond its equilibrium value. There is also a sensitivity enhancement in the rapid pulsing regime, where recovery is always incomplete. This sensitivity enhancement is illustrated with the one-dimensional double pulsed field gradient spin echo NOE experiment to observe a "fourth-order" NOE. Sensitivity gains of 30% are demonstrated.

Chemistry, Organic↗

PubMed1998

Improved cross peak detection in two-dimensional proton NMR spectra using excitation sculpting.

In two-dimensional homonuclear experiments, reliable detection of very small cross peaks is sometimes hampered by t1-noise from larger diagonal peaks which have the same F2 frequency. This t1-noise can be selectively removed by recording partial 2D spectra using the double pulsed field gradient spin echo (DPFGSE). Resonances not selected by the DPFGSE do not contribute any t1-noise to the resulting spectrum. The absence of t1-noise from the diagonal peaks render the small cross peaks at the same F2 frequency observable. The success of this technique is shown by partial 2D NOESY and TOCSY spectra.

Artifacts↗

PubMed1998

Reference deconvolution, phase correction, and line listing of NMR spectra by the 1D filter diagonalization method.

We describe a new way to attack the problem of identifying and quantifying the number of NMR transitions in a given NMR spectrum. The goal is to reduce the spectrum to a tabular line list of peak positions, widths, amplitudes, and phases, and to have this line list be of high fidelity. In this context "high fidelity" means that each true NMR transition is represented by a single entry, with no spurious entries and no missed peaks. A high fidelity line list allows the measurement of chemical shifts and coupling constants with good accuracy and precision and is the ultimate in data compression. There are two parts to the problem. The first is to overcome common imperfections: the non-Lorentzian lineshapes that can arise whenever the magnetic field inhomogeneity is less than perfect, and nonzero time delays that cause frequency-dependent phase errors. The second is to fit the spectral features to a model of Lorentzian lines. We use the recently developed filter diagonalization method (FDM) to accomplish the reference deconvolution, the phase correction, and the fitting, and show good progress toward the goal of obtaining a high fidelity line list.

Fourier Analysis↗

PubMed1998

Multiple-pulse mixing sequences that selectively enhance chemical exchange or cross-relaxation peaks in high-resolution NMR spectra.

Rotating-frame NMR experiments which either emphasize or suppress cross relaxation, and which simultaneously suppress TOCSY, COSY, and zero-quantum peaks in NMR spectra, are presented and analyzed. The new experiments rely on mixing sequences which follow naturally from the transverse-ROESY (Tr-ROESY) sequence of Hwang and Shaka, and which are applicable to larger molecules in solution (spin diffusion limit). In the first variant a modified Tr-ROESY sequence, called multiple-pulse ROESY (MP-ROESY), is used to enhance cross-relaxation peak intensity compared to Tr-ROESY; in the second, called phase-modulated CLEAN chemical exchange (CLEANEX-PM), cross-relaxation peaks are greatly attenuated. The two methods are thus complementary: MP-ROESY is used to observe Overhauser peaks, and CLEANEX-PM is used to eliminate them, permitting clear observation of chemical exchange peaks alone. The new techniques are examined by theory and experiment. Practical guidelines that will result in high-quality spectra are given, including the judicious use of continuous weak static magnetic field gradients.

Magnetic Resonance Spectroscopy↗

PubMed1998

Design and synthesis of a transition state analogue for the Diels-Alder reaction.

This paper describes the design and synthesis of a tricationic transition state analogue (TSA 1) for the Diels-Alder reaction. TSA 1 contains a bicyclo[2.2.1]heptene ring system that mimics the boat conformation of the Diels-Alder transition state and is designed to bind tightly to antibodies, nucleic acids, and imprinted polymers by means of hydrogen bonds and salt-bridges. This paper also describes the syntheses of the Diels-Alder reaction substrates (diene 2 and dienophile 3) and a sensitive HPLC assay to monitor the formation of Diels-Alder product 4. In contrast to previously reported TSAs and dienophiles for the Diels-Alder reaction that are based upon maleimides, TSA 1 and dienophile 3 are based upon fumaramide. The fumaramide system should destabilize the initially formed boat conformer of Diels-Alder product 4 and stabilize a half-chair conformer. The conversion of the initially formed boat conformer to the half-chair conformer is designed to help prevent Diels-Alder product 4 from binding strongly to catalysts selected to strongly bind TSA 1. This feature should minimize product inhibition, which can be a problem in the catalysis of the Diels-Alder reaction.

Bridged Bicyclo Compounds↗

PubMed1998

Stabilization of a C7 equatorial gamma turn in DMSO-d6 by a ditryptophan crosslink.

Covalent crosslinks can control local peptide conformation. In tripeptide sequences of the general formula Cys-Xxx-Cys, cysteine disulfides have been previously shown to enforce a C7 equatorial gamma-turn conformation (also referred to as an inverse gamma-turn). Much less is known about the effects of dityrosine and ditryptophan crosslinks on local peptide structure. In a series of tripeptides, ditryptophan crosslinks were formed using the two-step process of acid-promoted Mannich dimerization followed by oxidative aromatization. In these peptides, with the general formula Trp-Xxx-Trp (Xxx not equal to Gly), ditryptophan crosslinks were found to stabilize a C7 equatorial gamma-turn conformation in DMSO-d6. Rigorous support for a C7 equatorial conformation in the crosslinked sequence Trp-Pro-Trp came from a variety of 1H NMR experiments and molecular modelling. Interproton distances were derived from NOE buildups that were determined through a series of double pulsed field gradient spin echo (DPFGSE) experiments. In addition, the small temperature dependence of the i+2 NH chemical shifts (delta delta/delta T < 2 ppm/degree C) provided further support for the intramolecular hydrogen bond which defines a gamma-turn.

Cross-Linking Reagents↗