Conformational Analysis of Arabinofuranosides: Prediction of (3)JH,H Using MD Simulations with DFT-Derived Spin-Spin Coupling Profiles.

A molecular dynamics (MD) investigation on a series of oligo-α-arabinofuranosides (1-8) using the AMBER force field and the GLYCAM carbohydrate parameter set is reported. The validation of the method was carried out by direct comparison of experimental vicinal proton-proton coupling constants ((3)JH,H) with those obtained by using an empirically determined Karplus equation and density functional theory (DFT)-derived relationships specifically tailored for α-arabinofuranosyl systems. A simple code was developed to implement the determination of (3)JH,H by applying these relationships to the probability distributions of rotamers and ring conformations displayed by the simulations. The empirical Karplus relationship and the DFT-derived equations yielded, in most cases, the same trend as experiment for intra-ring (3)JH,H values. This direct comparison circumvents additional sources of errors that may arise from the assumptions introduced by the deconvolution procedures often used to calculate population of rotamers and ring conformations from experimental (3)JH,H.

The effectiveness of 1H decoupling in the 13C MAS NMR of paramagnetic solids: an experimental case study incorporating copper(II) amino acid complexes.

The use of continuous-wave (CW) 1H decoupling has generally provided little improvement in the 13C MAS NMR spectroscopy of paramagnetic organic solids. Recent solid-state 13C NMR studies have demonstrated that at rapid magic-angle spinning rates CW decoupling can result in reductions in signal-to-noise and that 1H decoupling should be omitted when acquiring 13C MAS NMR spectra of paramagnetic solids. However, studies of the effectiveness of modern 1H decoupling sequences are lacking, and the performance of such sequences over a variety of experimental conditions must be investigated before 1H decoupling is discounted altogether. We have studied the performance of several commonly used advanced decoupling pulse sequences, namely the TPPM, SPINAL-64, XiX, and eDROOPY sequences, in 13C MAS NMR experiments performed under four combinations of the magnetic field strength (7.05 or 11.75T), rotor frequency (15 or 30kHz), and 1H rf-field strength (71, 100, or 140kHz). The effectiveness of these sequences has been evaluated by comparing the 13C signal intensity, linewidth at half-height, LWHH, and coherence lifetimes, T2('), of the methine carbon of copper(II) bis(dl-alanine) monohydrate, Cu(ala)(2).H2O, and methylene carbon of copper(II) bis(dl-2-aminobutyrate), Cu(ambut)(2), obtained with the advanced sequences to those obtained without 1H decoupling, with CW decoupling, and for fully deuterium labelled samples. The latter have been used as model compounds with perfect 1H decoupling and provide a measure of the efficiency of the 1H decoupling sequence. Overall, the effectiveness of 1H decoupling depends strongly on the decoupling sequence utilized, the experimental conditions and the sample studied. Of the decoupling sequences studied, the XiX sequence consistently yielded the best results, although any of the advanced decoupling sequences strongly outperformed the CW sequence and provided improvements over no 1H decoupling. Experiments performed at 7.05T demonstrate that the XiX decoupling sequence is the least sensitive to changes in the 1H transmitter frequency and may explain the superior performance of this decoupling sequence. Overall, the most important factor in the effectiveness of 1H decoupling was the carbon type studied, with the methylene carbon of Cu(ambut)(2) being substantially more sensitive to 1H decoupling than the methine carbon of Cu(ala)(2).H2O. An analysis of the various broadening mechanisms contributing to 13C linewidths has been performed in order to rationalize the different sensitivities of the two carbon sites under the four experimental conditions.

Diastereomeric Xe chemical shifts in tethered cryptophane cages.

Cryptophane cages serve as host molecules to a Xe atom. Functionalization of cryptophane-A has permitted the development of Xe as a biosensor. Synthetic routes used to prepare cryptophanes result in racemic mixtures of the chiral cages. In the preparation of a tethered cryptophane-A cage for biosensor applications, some achiral and chiral substituents such as left-handed amino acids have been used. When the substituent is achiral, the NMR signal of the Xe atom in the functionalized cage in solution is a single isotropic peak, since the Xe shielding tensor components in the R and L cages differ by no more than the signs of the off-diagonal elements. Chiral substituents can split the cage-encapsulated Xe NMR signal into one or more sets of doublets, depending on the number of asymmetric centers in the substituent. We carry out quantum mechanical calculations of Xe nuclear magnetic shielding for the Xe atom at the same strategic position within an L cryptophane-A cage, under the influence of chiral potentials that represent r or l substituents outside the cage. Calculations of the Xe shielding response in the Lr and Ll diastereomeric pairs permit the prediction of the relative order of the Xe chemical shifts in solutions containing the Rl and Ll diastereomers. Where the substituent itself possesses two chiral centers, comparison of the calculated isotropic shielding responses in the Llr, Lrl, Rll, and Lrr systems, respectively, permits the prediction of the Xe spectrum of diastereomeric systems in solutions containing Llr, Rlr, Lll, and Rll systems. Assignment of the peaks observed in the experimental Xe NMR spectra is therefore possible, without having to undertake the difficult synthetic route that produces a single optically pure enantiomer.

Xe nuclear magnetic resonance line shapes in channels decorated with paramagnetic centers.

To make predictions of the Xe NMR line shapes for Xe in channels decorated with paramagnetic centers, we consider a model system using the O(2) molecule as the paramagnetic center. The previously calculated quantum mechanical Xe@O(2) hyperfine tensor for various configurations of Xe in the presence of O(2) provides a model for the hyperfine response of Xe atom to the presence of a paramagnetic center. The averaging is carried out using the same grand canonical Monte Carlo methodology as for calculating NMR line shapes for Xe in diamagnetic channels, modified to include the effects of the hyperfine tensor response. We explore the temperature dependence of the Xe line shapes, the dependence on the concentration, and the symmetry of distribution of embedded paramagnetic centers, on the orientation of the paramagnetic center axis with respect to the channel axis, and on the radial distance of the paramagnetic center from the axis of the channel. We predict Xe line shape signatures of the presence and orientation of paramagnetic centers and deduce which tensor elements provide measures of concentration and radial distance of paramagnetic centers from the channel axis.

Grand canonical Monte Carlo simulations of the 129Xe NMR line shapes of xenon adsorbed in (+/-)-[Co(en)3]Cl3.

The 129Xe NMR line shapes of xenon adsorbed in the nanochannels of the (+/-)-[Co(en)3]Cl3 ionic crystal have been calculated by grand canonical Monte Carlo (GCMC) simulations. The results of our GCMC simulations illustrate their utility in predicting 129Xe NMR chemical shifts in systems containing a transition metal. In particular, the nanochannels of (+/-)-[Co(en)3]Cl3 provide a simple, yet interesting, model system that serves as a building block toward understanding xenon chemical shifts in more complex porous materials containing transition metals. Using only the Xe-C and Xe-H potentials and shielding response functions derived from the Xe@CH4 van der Waals complex to model the interior of the channel, the GCMC simulations correctly predict the 129Xe NMR line shapes observed experimentally (Ueda, T.; Eguchi, T.; Nakamura, N.; Wasylishen, R. E. J. Phys. Chem. B 2003, 107, 180-185). At low xenon loading, the simulated 129Xe NMR line shape is axially symmetric with chemical-shift tensor components delta(parallel) = 379 ppm and delta(perpendicular) = 274 ppm. Although the simulated isotropic chemical shift, delta(iso) = 309 ppm, is overestimated, the anisotropy of the chemical-shift tensor is correctly predicted. The simulations provide an explanation for the observed trend in the 129Xe NMR line shapes as a function of the overhead xenon pressure: delta(perpendicular) increased from 274 to 292 ppm, while delta(parallel) changed by only 3 ppm over the entire xenon loading range. The overestimation of the isotropic chemical shifts is explained based upon the results of quantum mechanical 129Xe shielding calculations of xenon interacting with an isolated (+/-)-[Co(en)3]Cl3 molecule. The xenon chemical shift is shown to be reduced by about 12% going from the Xe@[Co(en)3]Cl3 van der Waals complex to the Xe@C2H6 fragment.

Xe NMR lineshapes in channels of peptide molecular crystals.

To further an understanding of the nature of information available from Xe chemical shifts in cavities in biological systems, it would be advantageous to start with Xe in regular nanochannels that have well known ordered structures built from amino acid units. In this paper, we report the experimental observation of Xe NMR lineshapes in peptide channels, specifically the self-assembled nanochannels of the dipeptide L-Val-L-Ala and its retroanalog L-Ala-L-Val in the crystalline state. We carry out grand canonical Monte Carlo simulations of Xe in these channels to provide a physical understanding of the observed Xe lineshapes in these two systems.

NMR studies of peptide T, an inhibitor of HIV infectivity, in an aqueous environment.

The synthetic octapeptide peptide T (ASTTTNYT) has been shown to interfere with binding of the HIV-1 envelope glycoprotein gp120 to the chemokine receptor R5, thus preventing viral infection. This study investigated the degree of conformational order of two analogs of peptide T, one biologically active (D-Ala peptide T amide) and one inactive (D-Ala, D-Tyr peptide T amide) using nuclear magnetic resonance (NMR) spectroscopy in an aqueous environment, both in solution and in the frozen solid state. Standard solution NMR techniques such as DQFCOSY, HMQC, ROESY and inversion recovery measurements have been utilized to characterize these peptides. Solid state NMR experiments were likewise employed to study the peptides in a frozen glycerol:water mixture. The NMR results indicate that the monomeric form of both peptide T analogs have considerable conformational heterogeneity. Solid state NMR studies indicate aggregation of D-Ala peptide T, possibly into a beta-sheet structure, at concentrations higher than 10 mM.

Molecular dynamics averaging of Xe chemical shifts in liquids.

The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.

Nuclear magnetic shielding and chirality IV. The odd and even character of the shielding response to a chiral potential.

We investigate the odd and even character of the shielding response in a chiral molecule (modeled by a Ne8 helix) when subjected to a chiral potential. We establish that the diastereomeric splittings are a measure of odd powers of Vodd. Implications for diastereomeric, splittings of Xe in handed cages with handed tethers are discussed.

The Xe shielding surfaces for Xe interacting with linear molecules and spherical tops.

The 129Xe nuclear magnetic resonance spectrum of xenon in gas mixtures of Xe with other molecules provides a test of the ab initio surfaces for the intermolecular shielding of Xe in the presence of the other molecule. We examine the electron correlation contributions to the Xe-CO2, Xe-N2, Xe-CO, Xe-CH4, and Xe-CF4 shielding surfaces and test the calculations against the experimental temperature dependence of the density coefficients of the Xe chemical shift in the gas mixtures at infinite dilution in Xe. Comparisons with the gas phase data permit the refinement of site-site potential functions for Xe-N2, Xe-CO, and Xe-CF4 especially for atom-Xe distances in the range 3.5-6 A. With the atom-atom shielding surfaces and potential parameters obtained in the present work, construction of shielding surfaces and potentials for applications such as molecular dynamics averaging of Xe chemical shifts in liquid solvents containing CH3, CH2, CF3, and CF2 groups is possible.

Properties of selected S-nitrosothiols compared to nitrosylated WR-1065.

WR-1065 ([N-mercaptoethyl]-1-3-diaminopropane), the active form of the aminothiol drug Ethyol/Amifostine, protects against toxicity caused by radiation, chemotherapy and endotoxin. Because WR-1065 and other thiols readily bind nitric oxide (NO), injurious conditions or therapies that induce the production or mobilization of NO could alter the effects of WR-1065. S-Nitrosothiols were prepared from various thiols by a standard method to compare properties and stability. Heteromolecular quantum correlation 2D nuclear magnetic resonance was used to characterize nitrosylated glutathione (GSH) and WR-1065; both S- and N-nitrosothiols were observed, depending on the experimental conditions. Three categories of S-nitrosothiol stability were observed: (1) highly stable, with t(1/2) > 8 h, N-acetyl-L-cysteine nitrosothiol (t(1/2) 15 h) > GSH nitrosothiol (t(1/2) 8 h); (2) intermediate stability, t(1/2) approximately 2 h, cysteamine nitrosothiol and WR-1065 nitrosothiol; and (3) low stability, t(1/2) < 1 h, cysteine nitrosothiol and Captopril nitrosothiol. Similar relative rates were observed for Hg(+2)-induced denitrosylation: WR-1065 reacted faster than GSH nitrosothiol, while GSH nitrosothiol reacted faster than N-acetyl-L-cysteine nitrosothiol. Mostly mediated by mixed-NPSH disulfide formation, the activity of the redox-sensitive cysteine protease, cathepsin H, was inhibited by the S-nitrosothiols, with WR-1065 nitrosothiol > cysteine nitrosothiol > N-acetyl-L-cysteine nitrosothiol and GSH nitrosothiol. These observations indicate that, relative to other nitrosylated non-protein thiols, the S-nitrosothiol of WR-1065 is an unstable non-protein S-nitrosothiols with a high reactive potential in the modification of protein thiols.