J-coupling Values Research Articles

On using oscillating time-dependent restraints in MD simulation

The use of time-dependent restraints in molecular simulation in order to generate a conformational ensemble for molecules that is in accordance with measured ensemble averages for particular observable quantities is investigated. Using a model system consisting of liquid butane and the cyclic peptide antamanide the reproduction of particular average (3) J-coupling constant values in a molecular dynamics simulation is analysed. It is shown that the multiple-valuedness and the sizeable gradients of the Karplus curve relating (3) J-coupling constants measured in NMR experiments to the corresponding torsional-angle values cause severe problems when trying to restrain a (3) J-coupling constant to a value close to the extrema of the Karplus curve. The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling.

A spectroscopic and computational study of stereochemistry in 2-hydroxymutilin

A computational and spectroscopic study of two epimers of 2-hydroxymutilin was conducted to obtain assignments for the configuration of the carbon at the 2-position. Gas-phase structural models for ( R)- and ( S)-2-hydroxymutilin were optimized using density functional theory (DFT). These models were validated using internuclear distances measured from 1H nuclear Overhauser effect (NOE) build-up rates in CDCl 3 solution. The models were subsequently used to predict NMR parameters using the hybrid B3LYP density functional. After linear scaling, the agreement between predicted gas-phase and observed solution-state chemical shifts was sufficient for relative stereochemical assignments, with an average absolute error of 0.16 and 1.47 ppm for 1H and 13C shifts, respectively. 1H– 1H and 1H– 13C coupling constants were also predicted using the B3LYP functional with the aug-cc-p-VTZ-J basis set and compared to experimental values (measured by J-resolved and gradient J-HMBC experiments). The predicted coupling constants were within 10% of their experimental values in most cases, and like the chemical shielding, allowed for relative stereochemical assignments of the isomers. DFT prediction of coupling constants gave more useful information than empirical parameterizations. Although just one chiral center changes between the two isomers, with no consequent conformational change and only two affected NOE restraints, predictable effects on 20 different chemical shielding and J-coupling values were observed. Including these values in the stereochemical assignment allows for additional confirmation of the stereochemical results, using data already available in 1D 1H spectra and 2D 1H– 13C correlation spectra. Electronic and vibrational circular dichroism (ECD and VCD) spectra of the two isomers are also measured and compared with theoretical predictions. VCD was especially useful for determining the absolute stereochemistry of 2-hydroxymutilin and was found to be superior to ECD in this role. The combination of computational and spectroscopic work is shown to be a useful tool in the analysis of unknown mutilin derivatives or other compounds, such as those present as minor impurities or metabolites in pharmaceutical samples.

NMR evidence of a spatially resolved oscillation in the Ef-LDOS in a nanoscale platinum electrocatalyst

Indirect nuclear spin–spin J-coupling measurements have been carried out on a conducting, carbon-supported 8.8 nm platinum electrocatalyst by using 195 Pt NMR. The J-coupling values show a marked variation across the spectrum. These J-coupling values were then transformed into the corresponding s-like Fermi level local density of states D s( E f, x), where x is the distance from the particle surface, revealing a spatially resolved oscillatory decay in D s( E f) which is responsible for the line broadening of the bulk peak in the 195 Pt NMR spectrum.

Proton NMR chemical shifts and coupling constants for brain metabolites.

Proton NMR chemical shift and J-coupling values are presented for 35 metabolites that can be detected by in vivo or in vitro NMR studies of mammalian brain. Measurements were obtained using high-field NMR spectra of metabolites in solution, under conditions typical for normal physiological temperature and pH. This information is presented with an accuracy that is suitable for computer simulation of metabolite spectra to be used as basis functions of a parametric spectral analysis procedure. This procedure is verified by the analysis of a rat brain extract spectrum, using the measured spectral parameters. In addition, the metabolite structures and example spectra are presented, and clinical applications and MR spectroscopic measurements of these metabolites are reviewed.

15N solid-state NMR studies of platinum ammine complexes

15N solid-state NMR spectroscopy has been used to study a range of platinum ammine complexes. Both the 15N chemical shifts and the 15N− 195Pt J-coupling values probe the platinum oxidation state, and are particularly useful in characterizing mixed-valence linear-chain complexes. Results are reported on platinum cis-diammine, trans-diammine and tetraammine complexes.

13C NMR assignments of the protonated carbons of [d(TAGCGCTA)]2 by two-dimensional proton-detected heteronuclear correlation.

The resonances of the protonated carbons of [d(TAGCGCTA)]2 have been assigned by the two-dimensional proton-detected double-quantum heteronuclear correlation experiment [( 1H-13C]-DQCOSY). 13C-coupled and 13C-decoupled versions of the experiment were used. The assignment method is discussed in detail. The deoxyribose cross peaks segregate into five well-resolved regions, and the base cross peaks have distinct features that are helpful for assignments. The cross peaks from the 1H-13C pairs at the Cyd5, Ado2 and ThdCH3 base positions fall in separate regions of the spectrum from each other; they also are resolved from the closely spaced Ado8, Guo8, Cyd6 and Thd6. Additional parameters for distinction of the base signals are their differing J-coupling values and long-range coupling patterns.