Nuclear Spin Cross Relaxation Research Articles

Examination of Solvent Interactions with Trp-Cage in 1,1,1,3,3,3-Hexafluoro-2-propanol-water at 298 K through MD Simulations and Intermolecular Nuclear Overhauser Effects.

MD simulations of the peptide Trp-cage dissolved in 28% hexafluoroisopropanol (HFIP)-water have been carried out at 298 K with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross-relaxation. The work was motivated by the observation that most experimental fluoroalcohol-peptide cross-relaxation terms at 298 K are small, both positive and negative, and not always well predicted from simulations. The cross-relaxation terms for hydrogens of the caged tryptophan residue of Trp-cage are substantially negative, a result consistent with simulations. It was concluded that hexafluoroisopropanol interactions near this part of the peptide are particularly long-lived. While both HFIP and water are present in all regions of the simulation box, the composition of the solvent mixture is not homogeneous throughout the system. HFIP generally accumulates near the peptide surface, while water molecules are preferentially found in regions that are more than 1.5 nm from the surface of the peptide. However, some water remains in higher-than-expected amounts in the solvent layer surrounding 6Trp, 9Asp, Ser13, and Ser14 residues in the helical region of Trp-cage. As observed in simulations of this system at 278 K, HFIP molecules aggregate into clusters that continually form and re-form. Translational diffusion of both HFIP and water appears to be slowed near the surface of the peptide with reduction in diffusion near the 6Trp residue 2- to 3-fold larger than calculated for solvent interactions with other regions of Trp-cage.

Examination of Interactions of Hexafluoro-2-propanol with Trp-Cage in Hexafluoro-2-propanol-Water by MD Simulations and Intermolecular Nuclear Overhauser Effects.

All-atom molecular dynamic simulations of the peptide Trp-cage in 30% hexafluoro-2-propanol- water (V/V) at 278 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross relaxation. Force field parameters for HFIP reported by Fioroni et al. along with the fluorine parameters of the TFE5 model reported by this lab were used. Water was represented by the TIP5P-Ew model. Peptide modeling used the AMBER99SB-ILDN force field. Translational diffusion coefficients of solution components at 278 K were predicted to within 35% of experimental values using these parameter sets. The simulations indicate that the solvent mixture is not homogeneous, with HFIP molecules clustered into aggregates as large as 53 fluoroalcohol molecules. The solvent environment of surface atoms of Trp-cage fluctuates between being HFIP-rich and more water-rich about every 10 ns. In accord with previous studies by other groups, the average concentration of HFIP near the surface of the peptide is significantly enhanced over the concentration of HFIP in the bulk solvent. In the simulations, ∼7% of the initial contacts between HFIP molecules and Trp-cage develop into peptide-fluoroalcohol interactions that persist for times as long as 8 ns. Most of the available experimental nuclear spin cross-relaxation rates (ΣHF) for hydrogens of the Trp-cage in 30% HFIP-water are reproduced from the MD trajectories to within uncertainties of the experimental data and the simulations. However, a few calculated ΣHF values for hydrogens of the Trp-cage do not agree with experiment. These tend to be situations where long-lived peptide-HFIP interactions are predicted. The disagreements between observed and calculated ΣHF in these instances signal defects in the modeling parameters and procedures that are presently unrecognized.

Examination of Trifluoroethanol Interactions with Trp-Cage in Trifluoroethanol-Water at 298 K through Molecular Dynamics Simulations and Intermolecular Nuclear Overhauser Effects.

Molecular dynamics simulations of the protein model Trp-cage in 42% trifluoroethanol (TFE)-water at 298 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross-relaxation. The TFE5 model of TFE developed in a previous work was used with the TIP5P-Ew model of water. System densities and component translational diffusion coefficients predicted by the simulations were within 20% of the experimental values. Consideration of the calculated relative amounts of TFE and water surrounding the hydrogens of Trp-cage indicated that the composition of the solvent mixture beyond ∼1.5 nm from the van der Waals surface of the peptide is close to the composition of the bulk solvent, but as observed by others, TFE accumulates preferentially near the peptide surface. In the simulations, both TFE and water molecules make contacts with the peptide surface; water molecules predominate in contacts with the peptide backbone atoms and TFE molecules generally preferentially interact with side chains. Translational diffusion of solvent molecules appears to be slowed near the surface of the peptide. Depending on the location in the structure, TFE molecules form complexes with the peptide that may persist for up to ∼7 ns. Many of the peptide spin-solvent fluorine cross-relaxation parameters (ΣHF) for which experimental values are available are reasonably well-predicted from the simulations. However, the calculated ΣHF values were too small for some hydrogens of the 6Trp indole ring and the amino acid hydrogens near this residue in the native structure, whereas ΣHF values for hydrogens on the side chains of 1Asn, 4Ile, and 7Leu are too large. In 42% TFE-water, persistent conformations of Trp-cage are found, which differ from the conformation found in water by the orientation of the 3Tyr ring.

Unexpected change in NOE with increasing temperature: Crosstalk between chemical exchange and cross relaxation in a NiN2S2 complex

Typically, with increasing sample temperature the rotational correlation time of the molecule decreases, leading to a decrease in the relative nuclear Overhauser effect (NOE) enhancement. In characterizing the (O-ethyl-L-cysteinato)-Ni(II) in the solution state, the measured NOE enhancement increases with increasing sample temperature. This unexpected change is explained via crosstalk between nuclear spin cross relaxation and an additional chemical exchange phenomenon between the amino protons of the molecule. The case study using a relaxation matrix approach, with both cross relaxation and chemical exchange, could be essential to understanding a metal complex with a bidentate amino acid derived ligands.

Examination of Trifluoroethanol Interactions with Trp-Cage through MD Simulations and Intermolecular Nuclear Overhauser Effects.

Molecular dynamics simulations of the protein model Trp-cage in 42% 2,2,2-trifluoroethanol (TFE)-water at 318 K have been carried out with the goal of exploring solvent fluorine-peptide hydrogen nuclear spin cross-relaxation. TFE5 and TFE6 models of TFE developed in previous work from this laboratory were used with the TIP5PE model of water. System densities and component translational diffusion coefficients were well predicted by the simulations, as were many of the cross-relaxation parameters (ΣHF) for which experimental values are available. However, the calculated ΣHF values were too small for some hydrogens of the Trp6 indole ring and for amino acid hydrogens near this residue in the native structure. Simulations carried out with unfolded versions of Trp-cage suggest that underestimates of ΣHF are the result of insufficient sampling of conformational motions that expose these hydrogens to interactions with solvent molecules during simulations of the native peptide. Consideration of the relative amounts of TFE and water surrounding the Trp-cage structure indicates that the composition of the solvent mixture at distances beyond ∼1.5 nm from the surface of the peptide is close to the composition of the bulk solvent, but, as observed by others, TFE tends to accumulate preferentially near the surface of the peptide. Both TFE and water molecules make contacts with the peptide surface; water molecules predominate in contacts with the peptide backbone atoms, and TFE molecules generally preferentially interact with side chains. Translational diffusion of solvent molecules appears to slow down near the surface of the peptide.

Limiting factor of defect-engineered spin-filtering effect at room temperature

We identify hyperfine-induced electron and nuclear spin cross-relaxation as the dominant physical mechanism for the longitudinal electron spin relaxation time $\left({T}_{1}\right)$ of the spin-filtering $G{a}_{i}^{2+}$ defects in GaNAs alloys. This conclusion is based on our experimental findings that ${T}_{1}$ is insensitive to temperature over 4--300 K, and its exact value is directly correlated with the hyperfine coupling strength of the defects that varies between different configurations of the $G{a}_{i}^{2+}$ defects present in the alloys. These results thus provide a guideline for further improvements of the spin-filtering efficiency by optimizing growth and processing conditions to preferably incorporate the $G{a}_{i}^{2+}$ defects with a weak hyperfine interaction and by searching for new spin-filtering defects with zero nuclear spin.

Enhancement of nuclear-spin cross-relaxation in metal-hydrogen systems.

A cross-relaxation model has previously been proposed to explain the anomalous frequency dependence of proton relaxation rates ${\mathit{R}}_{1}$ in several metal-hydrogen systems at low temperatures. We report two experiments that test and unambiguously confirm the cross-relaxation model. The first experiment uses large-amplitude field modulation to sweep the proton resonance through the inhomogeneously broadened spectrum of metal resonances. The second involves rotation of the sample to sweep the metal resonances through the proton line. In both experiments, the protons are brought into spin thermal contact with an increased number of metal nuclei. Sample rotation rates of only 10 Hz increase the proton ${\mathit{R}}_{1}$ by a factor of 50 for the ${\mathrm{TaH}}_{\mathit{x}}$ system. A simple model explains the variation of ${\mathit{R}}_{1}$ with rotation speed. Both techniques reveal increased proton relaxation rates ${\mathit{R}}_{1}$, unique signatures of the cross-relaxation model. A model is presented that explains the weaker than linear temperature dependence of ${\mathit{R}}_{1}$. The role of disorder on a length scale of 500 \AA{} or less is emphasized.

Novel measurements of nuclear spin cross-relaxation in metal hydrides

Recent NMR measurements of proton relaxation have shown an unexpected frequency dependence in several metal-hydrogen systems at low temperatures. An explanation proposed by the Ames group involves cross-relaxation of protons to quadrupolar metal nuclei. We test this hypothesis with relaxation experiments involving large amplitude field modulation. The field modulation sweeps the proton resonance through the distribution of metal frequencies. Thus the protons come into contact with more metal nuclei, increasing the proton relaxation rate. Relaxation measurements have been performed on several samples and the proton resonance frequency, the modulation frequency and the modulation amplitude have been varied. Also, proton relaxation rates T 1 −1 have been measured on slowly spinning samples where the rotation produces periodic variations of the metal quadrupolar frequencies.

Novel measurements of nuclear spin cross-relaxation in metal hydrides

Recent NMR measurements of proton relaxation have shown an unexpected frequency dependence in several metal-hydrogen systems at low temperatures. An explanation proposed by the Ames group involves cross-relaxation of protons to quadrupolar metal nuclei. We test this hypothesis with relaxation experiments involving large amplitude field modulation. The field modulation sweeps the proton resonance through the distribution of metal frequencies. Thus the protons come into contact with more metal nuclei, increasing the proton relaxation rate. Relaxation measurements have been performed on several samples and the proton resonance frequency, the modulation frequency and the modulation amplitude have been varied. Also, proton relaxation rates T 1 −1 have been measured on slowly spinning samples where the rotation produces periodic variations of the metal quadrupolar frequencies.

A possible overhauser mechanism for 19F nuclear spin polarization in the reaction of fluorobenzyl halides with sodium naphthalene

It is proposed that the high field 19F nuclear spin polarization observed in the product of the reaction of fluorobenzyl halides with sodium naphthalene is not due to the usual radical pair mechanism, but rather to a build up of electron spin polarization in the intermediate benzyl radical combined with electron—nuclear spin cross relaxation.