NMR Response Research Articles

Insights into the Photoprotective Switch of the Major Light-harvesting Complex II (LHCII): A PRESERVED CORE OF ARGININE-GLUTAMATE INTERLOCKED HELICES COMPLEMENTED BY ADJUSTABLE LOOPS

Light-harvesting antennae of the LHC family form transmembrane three-helix bundles of which two helices are interlocked by conserved arginine-glutamate (Arg-Glu) ion pairs that form ligation sites for chlorophylls. The antenna proteins of photosystem II have an intriguing dual function. In excess light, they can switch their conformation from a light-harvesting into a photoprotective state, in which the excess and harmful excitation energies are safely dissipated as heat. Here we applied magic angle spinning NMR and selective Arg isotope enrichment as a noninvasive method to analyze the Arg structures of the major light-harvesting complex II (LHCII). The conformations of the Arg residues that interlock helix A and B appear to be preserved in the light-harvesting and photoprotective state. Several Arg residues have very downfield-shifted proton NMR responses, indicating that they stabilize the complex by strong hydrogen bonds. For the Arg Cα chemical shifts, differences are observed between LHCII in the active, light-harvesting and in the photoprotective, quenched state. These differences are attributed to a conformational change of the Arg residue in the stromal loop region. We conclude that the interlocked helices of LHCII form a rigid core. Consequently, the LHCII conformational switch does not involve changes in A/B helix tilting but likely involves rearrangements of the loops and helical segments close to the stromal and lumenal ends.

An NMR comparison of the light-harvesting complex II (LHCII) in active and photoprotective states reveals subtle changes in the chlorophyll a ground-state electronic structures

To protect the photosynthetic apparatus against photo-damage in high sunlight, the photosynthetic antenna of oxygenic organisms can switch from a light-harvesting to a photoprotective mode through the process of non-photochemical quenching (NPQ). There is growing evidence that light-harvesting proteins of photosystem II participate in photoprotection by a built-in capacity to switch their conformation between light-harvesting and energy-dissipating states. Here we applied high-resolution Magic-Angle Spinning Nuclear Magnetic Resonance on uniformly 13C-enriched major light-harvesting complex II (LHCII) of Chlamydomonas reinhardtii in active or quenched states. Our results reveal that the switch into a dissipative state is accompanied by subtle changes in the chlorophyll (Chl) a ground-state electronic structures that affect their NMR responses, particularly for the macrocycle 13C4, 13C5 and 13C6 carbon atoms. Inspection of the LHCII X-ray structures shows that of the Chl molecules in the terminal emitter domain, where excited-state energy accumulates prior to further transfer or dissipation, the C4, 5 and 6 atoms are in closest proximity to lutein; supporting quenching mechanisms that involve altered Chl–lutein interactions in the dissipative state. In addition the observed changes could represent altered interactions between Chla and neoxanthin, which alters its configuration under NPQ conditions. The Chls appear to have increased dynamics in unquenched, detergent-solubilized LHCII. Our work demonstrates that solid-state Nuclear Magnetic Resonance is applicable to investigate high-resolution structural details of light-harvesting proteins in varied functional conditions, and represents a valuable tool to address their molecular plasticity associated with photoprotection.

Numerical simulation of (T 2, T 1) 2D NMR and fluid responses

One-dimensional nuclear magnetic resonance (1D NMR) logging technology is limited for fluid typing, while two-dimensional nuclear magnetic resonance (2D NMR) logging can provide more parameters including longitudinal relaxation time (T 1) and transverse relaxation time (T 2) relative to fluid types in porous media. Based on the 2D NMR relaxation mechanism in a gradient magnetic field, echo train simulation and 2D NMR inversion are discussed in detail. For 2D NMR inversion, a hybrid inversion method is proposed based on the damping least squares method (LSQR) and an improved truncated singular value decomposition (TSVD) algorithm. A series of spin echoes are first simulated with multiple waiting times (T W s) in a gradient magnetic field for given fluid models and these synthesized echo trains are inverted by the hybrid method. The inversion results are consistent with given models. Moreover, the numerical simulation of various fluid models such as the gas-water, light oil-water, and vicious oil-water models were carried out with different echo spacings (T E s) and T W s by this hybrid method. Finally, the influences of different signal-to-noise ratios (SNRs) on inversion results in various fluid models are studied. The numerical simulations show that the hybrid method and optimized observation parameters are applicable to fluid typing of gas-water and oil-water models.

The Scaling Law between Molecular Mass and Diffusivity and its Influence on the Molecular Weight Distribution as Derived from a Stretched Exponential PGSTE NMR Response Curve

AbstractThe molecular weight distribution characteristics derived from an inverse Laplace transformation (ILT) of a stretched exponential PGSTE NMR response function (SEF) is discussed with reference to the scaling law between diffusivity (D) and molecular mass (M) (D = KM−α). Two general equations are presented, enabling the polydispersity index (PDI) and the average molecular weights (Mw, Mn, and Mmed) to be determined from α and the two characteristic parameters β and D0 of the (normalized) SEF (= exp [(−D0t)β]). A detailed discussion regarding the derivation of the two equations is presented.

Surface-NMR measurements of the longitudinal relaxation time T1 in a homogeneous sand aquifer in Skive, Denmark

Surface nuclear magnetic resonance (surface NMR) is a geophysical technique used in the exploration of shallow aquifers. It is based on measuring the NMR response of water molecules to excitation by electromagnetic pulses. By increasing the moment of applied pulses, successively deeper regions of an aquifer can be probed. The longitudinal relaxation time T1, determined from the NMR experiment, depends on pore size and can be potentially used to estimate hydraulic conductivity. A novel scheme was recently proposed that was shown theoretically to be more reliable for acquiring surface-NMR T1 data than traditional acquisition. In this proof-of-concept study we provide the first empirical evidence for the superiority of the novel scheme. We chose a survey site close to Skive, Denmark, where proximate boreholes indicate a homogeneous sandy aquifer in the top 30 m. The homogeneous composition implies that the distribution of pore sizes does not vary significantly across the formation. Because pore size is reflected by the T1 relaxation time, we therefore assume that the homogeneous aquifer can be characterized by a single T1 independent of the applied pulse moment (i.e., sampled depth region)—this is the benchmark condition we tested with our surface-NMR measurements. We collected surface-NMR T1 data employing the traditional as well as the novel acquisition scheme at various pulse moments. For each pulse moment we infer a T1 relaxation time based on extensively sampled data (14 delay-time data points). The T1 relaxation times obtained using the novel scheme show a constant value of about 820 ms (± 38 ms) for all pulse moments. In contrast, the T1 relaxation times determined using the traditional scheme vary significantly between 530 and 750 ms with pulse moment, which in an inversion would result in a spatial variation of T1 across the aquifer. The results based on the novel scheme are consistent with a homogeneous aquifer, which we expect based on the borehole information, whereas the variation of T1 obtained by the traditional scheme could be misinterpreted as a variation of pore size or hydraulic conductivity.

On the sensitivity of surface NMR in the presence of electrical conductivity anomalies

The surface-NMR tomography technique is based on the principles of electromagnetic induction and proton spin dynamics. Electromagnetic fields emitted by large surface current-driven loops are employed to locate and quantify groundwater reservoirs. The oscillating magnetic fields interact with proton spins of water molecules in the electrically conductive subsurface. To study the influence of changing subsurface electrical properties on the nuclear spin response, we consider the spin magnetization as a virtual magnetic dipole receiver. The numerical solutions for the electric and magnetic fields of the transmitter and the virtual receiver in 3-D heterogeneous ground are based on the finite-element method. We explicitly compute the frequency-domain electromagnetic sensitivities for separate spin magnetizations in a groundwater aquifer to study the distortion of the NMR response because of electrical heterogeneities in the medium. Analyses of entire pulse moment sequences yield the cumulative sensitivities to electrical conductivity and water-content variations in the subsurface. We illustrate the influence of conductivity on NMR responses using a limited number of models. From these models we found that electrical conductivity anomalies in the shallow subsurface (<50 m) having values =0.1 S m-1 and volumes with linear dimensions in the order of our loop size (i.e. edge length 100 m) can have a strong influence on the NMR response and ought to be taken into account in the inversion of surface-NMR data. The effect increases non-linearly with increased body size, increased conductivity contrast and decreased anomaly depth.

Corrections for downhole NMR logging

Nuclear magnetic resonance logging (NMR) is an open well logging method. Drilling mud resistivity, formation resistivity and sodium ions influence its radio frequency (RF) field strength and NMR logging signals. Research on these effects can provide an important basis for NMR logging data acquisition and interpretation. Three models, water-based drilling mud—water bearing formation, water-based drilling mud—oil bearing formation, oil-based drilling mud—water bearing formation, were studied by finite element method numerical simulation. The influences of drilling mud resistivity and formation resistivity on the NMR logging tool RF field and the influences of sodium ions on the NMR logging signals were simulated numerically. On the basis of analysis, RF field correction and sodium ion correction formulae were proposed and their application range was also discussed. The results indicate that when drilling mud resistivity and formation resistivity are 0.02 Ω·m and 0.2 Ω·m respectively, the attenuation index of centric NMR logging tool is 8.9% and 9.47% respectively. The RF field of an eccentric NMR logging tool is affected mainly by formation resistivity. When formation resistivity is 0.1 Ω·m, the attenuation index is 17.5%. For centric NMR logging tools, the signals coming from sodium ions can be up to 31.8% of total signal. Suggestions are proposed for further research into NMR logging tool correction method and response characteristics.

Molecular Weight Distribution Characteristics (of a Polymer) Derived from a Stretched‐Exponential PGSTE NMR Response Function—Simulation

AbstractAssuming the signal response in a pulsed gradient stimulated echo (PGSTE) experiment (on a polymer) to be described by a simple stretched‐exponential function (SEF) and knowing the scaling law between diffusivity and molecular weight, the molecular weight distribution (MWD) characteristics (kurtosis, skewness, moment, and width) are derived and compared to the corresponding distribution characteristics obtained by a log‐normal function fit (to the same MWD). Also, the challenge involved in obtaining a reliable weight average molecular weight from an SEF response function is discussed.

A receptor incorporating OH, NH and CH binding motifs for a fluoride selective chemosensor

An anion receptor combined different types of hydrogen bond donors such as OH, NH and CH groups has been synthesized. By rotation of the sub methyl group, this receptor showed evident (1)H NMR response to both fluoride and sulfate, while colorimetric and fluorescent responses were only observed in the presence of fluoride.

Selective excitation in Fourier transform nuclear magnetic resonance

The applications of frequency-selective excitation methods in Fourier transform NMR are discussed, and a simple technique is described for selective excitation of a narrow frequency region of a high-resolution NMR spectrum in a Fourier transform spectrometer. A regular sequence of identical radiofrequency pulses of small flip angle exerts a strong cumulative effect on magnetizations close to resonance with the transmitter frequency or one of a set of equally spaced sidebands separated by the pulse repetition rate. All other magnetizations precess through an incomplete number of full rotations between pulses, and are caught by successive pulses at an ever changing phase of their precession, which destroys the cumulative effect. The motion of the various nuclear magnetization vectors may be described pictorially according to the Bloch equations, neglecting relaxation during the pulse sequence. A general theory is presented for selective or “tailored” excitation by an arbitrary modulation of the radiofrequency transmitter signal. It confirms earlier conclusions that the frequency-domain excitation spectrum corresponds to the Fourier transform of the transmitter modulation pattern, provided that the NMR response remains linear. The excitation spectra calculated for the selective pulse sequence by these two alternative approaches show good agreement within their respective limitations. A number of practical applications of selective excitation are explored, including solvent peak suppression, the detection of partial spectra from individual chemical sites, selective studies of relaxation and slow chemical exchange, and holeburning or localized saturation.

A Simple Access to the (Log/Normal) Molecular Weight Distribution Parameters of Polymers Using PGSTE NMR

AbstractA log/normal MWD is characterized by two parameters, its mean molecular weight M0 and width σ. It is demonstrated how these parameters can be obtained by model fitting a stretched exponential function (SEF), as characterized by two parameters β and DS, to the PGSTE response curve. Based on simulations, two general empirical equations relating β and DS to M0 and σ are found. The model enables the MWD characteristics to be determined if the scaling law between diffusivity and molecular weight is known. The sensitivity and relative error of σ and M0 are discussed and the applicability of the model is illustrated by analyzing experimental NMR response curve of some PEO samples. The key advantages of this technique are its simplicity, numerical robustness, and reliability. magnified image

Photophysical, electrochemical and anion sensing properties of Ru(ii) bipyridine complexes with 2,2′-biimidazole-like ligand

A new anion sensor [Ru(bpy)(2)(DMBbimH(2))](PF(6))(2) (3) (bpy is 2, 2'-bipyridine and DMBbimH(2) is 7,7'-dimethyl-2,2'-bibenzimidazole) has been developed. Its photophysical, electrochemical and anion sensing properties are compared with two previously investigated systems, [Ru(bpy)(2)(BiimH(2))](PF(6))(2) (1) and [Ru(bpy)(2)(BbimH(2))](PF(6))(2) (2) (BiimH(2) is 2,2'-biimidazole and BbimH(2) is 2,2'-bibenzimidazole). The high acidity of the N-H fragments in these complexes make them easy to be deprotonated by strong basic anions such as F(-) and OAc(-), and they form N-H···X hydrogen bonds with weak basic anions like Cl(-), Br(-), I(-), NO(3)(-), and HSO(4)(-). Complex 3 displays strong hydrogen bonding with these 5 weak basic anions, with binding constants between 17,000 and 21,000, which are larger than those observed in complex 1, with binding constants between 3300 and 5700, and in complex 2, which shows no hydrogen bonding toward Cl(-), Br(-), I(-), and NO(3)(-), and forms considerable hydrogen bonds with HSO(4)(-) with a binding constant of 11,209. These hydrogen bonding behaviours give different NMR, emission and electrochemical responses. The different anion binding affinity of these complexes may be mainly attributed to their different pK(a1) values, 7.2 for 1, 5.7 for 2, and 6.2 for 3. The additional methyl groups at the 7 and 7' positions of complex 3 may also play an important role in the enhancement of anion binding strength.

Synthesis, structure and solid state NMR analysis of a new templated titanium(III/IV) fluorophosphate

Abstract The title compound MIL-131 (MIL stands for Material from Institut Lavoisier) was prepared hydrothermally (4 days, 473 K, autogenous pressure) in the presence of an organic base (N((CH2)2NH2)3). The structure of MIL-131 or TiIIITiIV(OH)F4(HPO4)·(PO4)·(N((CH2)2NH3)3) has been determined ab initio from X-Ray synchrotron powder diffraction data using simulated annealing methods and was refined in the triclinic space group P-1 (no. 2). MIL-131 exhibits a one-dimensional structure built up from inorganic chains of corner sharing TiO5(OH) titanium(III) octahedra and PO4 and HPO4 phosphate tetrahedra, related to TiO2F4 titanium octahedra. Protonated triamine cations are located between the inorganic motifs, and interact strongly with the mineral network through hydrogen bondings both with terminal fluorine atoms and hydroxo or oxo groups. Multinuclear solid state NMR has allowed a clear attribution of the protons, fluoride, and phosphate groups environment within the framework of MIL-131. The large values of chemical shift anisotropy together with the absence of any 13C NMR response confirmed the presence of paramagnetic titanium(III) species deduced from the crystal structure. Finally, 2D MAS 1H-31P CP-HETCOR NMR correlation experiment gives some insight on the nature of the intra-framework hydrogen bonding. Crystal data for MIL-131: a = 14.109(1) A, b = 8.462(3) A, c = 7.179(1) A, α = 93.772(1)°, β = 96.566(2)°, γ = 98.004(1)°, V = 840.36(2) A3, z = 2.

Multinuclear NMR of CaSiO3 glass: simulation from first-principles

An integrated computational method which couples classical molecular dynamics simulations with density functional theory calculations is used to simulate the solid-state NMR spectra of amorphous CaSiO(3). Two CaSiO(3) glass models are obtained by shell-model molecular dynamics simulations, successively relaxed at the GGA-PBE level of theory. The calculation of the NMR parameters (chemical shielding and quadrupolar parameters), which are then used to simulate solid-state 1D and 2D-NMR spectra of silicon-29, oxygen-17 and calcium-43, is achieved by the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods. It is shown that the limitations due to the finite size of the MD models can be overcome using a Kernel Estimation Density (KDE) approach to simulate the spectra since it better accounts for the disorder effects on the NMR parameter distribution. KDE allows reconstructing a smoothed NMR parameter distribution from the MD/GIPAW data. Simulated NMR spectra calculated with the present approach are found to be in excellent agreement with the experimental data. This further validates the CaSiO(3) structural model obtained by MD simulations allowing the inference of relationships between structural data and NMR response. The methods used to simulate 1D and 2D-NMR spectra from MD GIPAW data have been integrated in a package (called fpNMR) freely available on request.

Magnetic Susceptibility of Heavy Fermion 3He-Bilayers

A 3He bilayer film adsorbed on graphite preplated with a bilayer of solid 4He has recently been shown to be a new heavy fermion system that can be tuned towards a quantum critical point (QCP) by varying the 3He coverage. We report new measurements of the temperature dependence of the magnetic susceptibility of this system over the temperature range 0.3 to 300 mK. The magnetisation of the 3He film is measured using pulsed NMR at a frequency of 60 kHz, on a SQUID detector setup with an untuned input circuit. The signal sensitivity attainable with this setup enables us to collect high-precision data with reasonable acquisition times, despite the low surface area of the sample (2 m2) and the small liquid susceptibility. The detailed NMR response provides an essential diagnostic tool to precisely adjust the 4He preplating. On cooling, the magnetisation evolves from Curie-law, through a distinct Kondo-like maximum at a temperature T*, to a weakly rising magnetisation far below the Curie law. This behaviour signifies the formation of the heavy fermion state of the coupled 3He layers. As the 3He coverage is increased towards the putative QCP, T* is tuned to lower temperature. These preliminary observations demonstrate the power of the technique, confirm previous results obtained in a different sample cell by a different method, and pave the way for a detailed study close to the QCP.

Superfluid 3He Confined in a Single 0.6 Micron Slab

We present the preliminary results of our studies of superfluid 3He in a 0.6 μm thick slab using NMR. Below Tc the A phase is observed, and at low pressures the region of stability of the A phase extends down to the lowest temperatures reached, as described elsewhere. At pressures above 3.2 bar another, so far unidentified phase is observed at low temperatures. In this article we focus on the behavior of this phase and the transition between this phase and the A phase, all studied at 5.5 bar. The NMR response at low temperatures exhibits two possible frequency shifts and the transition is hysteretic in temperature.

Transiently Trapped Entanglements in Model Polymer Networks

The relaxational dynamics of trapped entanglements in model silicone polymer networks is studied through the residual dipolar couplings (RDC) obtained by double quantum nuclear magnetic resonance (DQ NMR). These experiments were performed on model polymer networks containing linear pendant chains. The model networks where synthesized by end-linking a mixture of α,ω-divinyl poly(dimethylsiloxane) (B2) and ω-vinyl poly(dimethylsiloxane) (B1) with trifunctional (A3) or tetra-functional (A4) cross-linkers. At the time scale of the NMR experiments only a small fraction of the linear pendant chains B1 loses the memory of its early configuration. Then, the unrelaxed topological constrains involving pendant material render a nonzero average dipolar coupling that contributes to the solid-like behavior of the NMR response. Irrespective of the functionality of the cross-linkers, upon the presence in the network of pendant chains induced by the insertion of the B1 monofunctional poly(dimethylsiloxane) an important re...

Pore-scale simulation of NMR response

The random walk method is used to simulate magnetization decay in porous media. The simulations were performed on images of the pore space obtained using micro-CT scanning and in topologically equivalent networks extracted from these images using a maximal ball algorithm. The simulation results were validated through comparison with experimental measurements of T 2 distribution, absolute permeability and resistivity in two sand packs and from comparing predictions on images and networks of Fontainebleau sandstone. In all cases, the comparisons were good, although the networks gave a slightly narrower T 2 distribution, implying that some fine detail of the pore structure was lost. This work suggests that imaging, network extraction and pore-scale simulation can be used to predict single-phase transport properties successfully. It serves as a validation for pore-network models and the methods used to generate networks.

Use of rotary echoes in [formula omitted] magic-angle spinning NMR for the quantitative study of molecular dynamics

The interaction of sample spinning and chemical dynamics is analysed in the context of 2 H magic-angle spinning NMR. We develop previous analyses and show that a metric based on the intensity of rotational echoes allows kinetic information to be derived without the need for full modelling of the NMR response. This approach is illustrated on the conformational exchange of 1,4-dioxane included in the channel solvate hydrate formed with finasteride. An activation barrier in excellent agreement with previous experimental and theoretical estimates is obtained, without the need for modelling which would be very challenging due to the anisotropic tumbling of the solvent molecules.

Improved Interpretation of Nuclear Magnetic Resonance T1 and T2 Distributions for Permeability Prediction: Simulation of Diffusion Coupling for a Fractal Cluster of Pores

NMR relaxometry is a powerful tool for inferring porosity and permeability data. In practice, measured magnetization decay curves are inverted for relaxation time distributions. Subsequently, one presumes a linear relationship between the pore radius distribution and the T1 and T2 distribution, for longitudinal and transverse magnetization, respectively. The fundamental equations used are based on a pore model, in which pores are assumed to be isolated from each other with respect to the NMR process and have smooth walls. The present study is based on a geometrical pore space model with connected pores and structured pore walls. The physical processes of surface relaxation, irreversible dephasing of magnetic spins and diffusive proton exchange between pores, are described by a system of differential equations. The solution yields a set of exponential functions representing the relaxation time distribution. We describe the difference between the distributions obtained for diffusion coupling and for isolated pores. With diffusion coupling on, the spectral width of the T1 distribution is strongly reduced, which indicates that the influence of large and small radii according to the T1-pore radius relationship is mixed to some extent. For a fractal pore space structure, where large pores are surrounded by adjacent minor pores, the T1 distribution does not resolve these substructures. Nevertheless, permeability values calculated from the logarithmic mean relaxation time T1,LM are quite the same for diffusion coupling and for isolated pores. The T2 distribution for diffusion coupling is little constricted and gives a better resolution of the pore wall structures than the corresponding T1 distribution. The permeability values from T2 distributions agree with the values from longitudinal magnetization, provided that we use a corrected relaxation time T2,corr, accounting for the dependence of the surface relaxivity ρ2 on pore radius. The study shows that radius distributions calculated from a T1 and from a T2 distribution differ from one another and both present an altered image of the true pore radius distribution. In practice, this has no serious influence on estimating permeability of medium- to high-permeability sandstones with the currently applied methods. The presented methodology of calculating the NMR response of pore space models with diffusion coupling may facilitate understanding porosity-permeability relationships of different rock types such as carbonate rocks with micro-porosity.