Dipolar Correlation Research Articles

Integrating 19F Distance Restraints for Accurate Protein Structure Determination by Magic Angle Spinning NMR Spectroscopy.

Traditional protein structure determination by magic angle spinning (MAS) solid-state NMR spectroscopy primarily relies on interatomic distances up to 8 Å, extracted from 13C-, 15N-, and 1H-based dipolar-based correlation experiments. Here, we show that 19F fast (60 kHz) MAS NMR spectroscopy can supply additional, longer distances. Using 4F-Trp,U-13C,15N crystalline Oscillatoria agardhii agglutinin (OAA), we demonstrate that judiciously designed 2D and 3D 19F-based dipolar correlation experiments such as (H)CF, (H)CHF, and FF can yield interatomic distances in the 8-16 Å range. Incorporation of fluorine-based restraints into structure calculation improved the precision of Trp side chain conformations as well as regions in the protein around the fluorine containing residues, with notable improvements observed for residues in proximity to the Trp pairs (W10/W17 and W77/W84) in the carbohydrate-binding loops, which lacked sufficient long-range 13C-13C distance restraints. Our work highlights the use of fluorine and 19F fast MAS NMR spectroscopy as a powerful structural biology tool.

Markers of low field NMR relaxation features of tissues

This work presents an approach to exploiting Nuclear Magnetic Resonance (NMR) relaxometry data (1H spin-lattice relaxation rates covering the frequency range from below 1 kHz to 10 MHz) for the purpose of differentiating between pathological and reference tissues. Characteristic quantities (markers) that can be obtained in a straightforward manner, not resorting to an advanced analysis of 1H spin-lattice relaxation data, have been identified and compared for pathological and reference colon tissues. Moreover, the relaxation data have been parametrised in terms of Lorentzian spectral densities and the possibility of using the obtained dipolar relaxation constants and correlation times as biomarkers to assess the state of tissues has been discussed. It has also been demonstrated that the relaxation data for the reference and the pathological tissues can be attributed to two groups (for each case). The studies are a step towards exploiting the potential of NMR relaxometry for characterisation of pathological changes in tissues.

Expanding the tool box for native structural biology: 19F dynamic nuclear polarization with fast magic angle spinning.

Obtaining atomic-level information on components in the cell is a major focus in structural biology. Elucidating specific structural and dynamic features of proteins and their interactions in the cellular context is crucial for understanding cellular processes. We introduce 19F dynamic nuclear polarization (DNP) combined with fast magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy as a powerful technique to study proteins in mammalian cells. We demonstrate our approach on the severe acute respiratory syndrome coronavirus 2 5F-Trp-NNTD protein, electroporated into human cells. DNP signal enhancements of 30- to 40-fold were observed, translating into over 1000-fold experimental time savings. High signal-to-noise ratio spectra were acquired on nanomole quantities of a protein in cells in minutes. 2D 19F-19F dipolar correlation spectra with remarkable sensitivity and resolution were obtained, exhibiting 19F-19F cross peaks associated with fluorine atoms as far as ~10 angstroms apart. This work paves the way for 19F DNP-enhanced MAS NMR applications in cells for probing protein structure, dynamics, and ligand interactions.

Effect of lithium concentration on the network connectivity of nuclear waste glasses

Structure of borosilicate glasses with varying Li2O contents were investigated using Magic Angle Spinning (MAS) Nuclear Magnetic Resonance (NMR), employing 6Li, 11B, 23Na, 27Al and 29Si nuclei. 11B MAS NMR revealed that increasing Li2O contents result in formation of [BO4]− sites at the expense of BO3. 11B{6Li} and 27Al{6Li} dipolar heteronuclear multiple quantum correlation (D-HMQC) NMR revealed Li as a charge compensator for anionic tetrahedral sites with increased Li. 11B{6Li} J-coupling mediated HMQC NMR suggested the possible association of Li with non-bridging oxygens on Q2 and Q3 sites, indicating its dual role in the glass network. 29Si and 23Na MAS NMR spectra showed depolymerisation of the silicate network and shortening of Na-O bond lengths with increased Li. NMR results are supported by Raman spectroscopy and thermal analysis that indicate depolymerisation of the silicate network and a reduction in glass transition temperature at higher Li content.

Atomic-Level Structure of the Organic-Inorganic Interface of Colloidal ZnO Nanoplatelets from Dynamic Nuclear Polarization-Enhanced NMR.

Colloidal semiconductor nanoplatelets (NPLs) have emerged as a new class of nanomaterials that can exhibit substantially distinct optical properties compared to those of isotropic quantum dots, which makes them prime candidates for new-generation optoelectronic devices. Insights into the structure and anisotropic growth of NPLs can offer a blueprint for their controlled fabrication. Here, we present an atomic-level investigation of the organic-inorganic interface structure in ultrathin and stable benzamidine (bza)-supported ZnO NPLs prepared by the modified one-pot self-supporting organometallic approach. High-resolution transmission electron microscopy analysis showed a well-faceted hexagonal shape of ZnO NPLs with lateral surfaces terminated by nonpolar (101̅0) facets. The basal surfaces are flat and well-formed on one side and corrugated on the other side, which indicates that the layer-by-layer growth in the thickness of the NPLs likely occurs only in one direction via the expansion of 2D islands on the surface. The ligand coordination modes were elucidated using state-of-the-art dynamic nuclear polarization (DNP)-enhanced solid-state NMR spectroscopy supported by density functional theory chemical shift calculations. Specifically, it was found that (101̅0) nonpolar facets are stabilized by neutral L-type bza-H ligands with hydrogen bond-supported η1-coordination mode, while polar (0001) and (0001̅) facets are covered by μ2-coordinated X-type anionic bza ligands with different conformations of aromatic rings. Moreover, the ligand packing on (101̅0) lateral facets was determined using 13C natural abundance (∼1.1%) homonuclear dipolar correlation experiments. Overall, an in-depth understanding of the growth mechanism and the unique bimodal X-type/L-type ligand coordination shell of ZnO NPLs is provided, which will facilitate further design of anisotropic nano-objects.

Sensitivity of Australian Rainfall to Driving SST Data Sets in a Variable‐Resolution Global Atmospheric Model

AbstractIn this study, we employ the Conformal Cubic Atmospheric Model (CCAM), a variable‐resolution global atmospheric model, driven by two distinct sea surface temperature (SST) data sets: the 0.25° Optimum Interpolation Sea Surface Temperature (CCAM_OISST) version 2.1 and the 2° Extended Reconstruction SSTs Version 5 (CCAM_ERSST5). Model performance is assessed using a benchmarking framework, revealing good agreement between both simulations and the climatological rainfall spatial pattern, seasonality, and annual trends obtained from the Australian Gridded Climate Data (AGCD). Notably, wet biases are identified in both simulations, with CCAM_OISST displaying a more pronounced bias. Furthermore, we have examined CCAM’s ability to capture El Niño‐Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) correlations with rainfall during Austral spring (SON) utilizing a novel hit rate metric. Results indicate that only CCAM_OISST successfully replicates observed SON ENSO‐ and IOD‐rainfall correlations, achieving hit rates of 86.6% and 87.5%, respectively, compared to 52.7% and 41.8% for CCAM_ERSST5. Large SST differences are found surrounding the Australian coastline between OISST and ERSST5 (termed the “Coastal Effect”). Differences can be induced by the spatial interpolation error due to the discrepancy between model and driving SST. An additional CCAM experiment, employing OISST with SST masked by ERSST5 in 5° proximity to the Australian continent, underscores the “Coastal Effect” has a significant impact on IOD‐Australian rainfall simulations. In contrast, its influence on ENSO‐Australian rainfall is limited. Therefore, simulations of IOD‐Australian rainfall teleconnection are sensitive to local SST representation along coastlines, probably dependent on the spatial resolution of driving SST.

19F Fast Magic-Angle Spinning NMR Spectroscopy on Microcrystalline Complexes of Fluorinated Ligands and the Carbohydrate Recognition Domain of Galectin-3.

Structural characterization of protein-ligand binding interfaces at atomic resolution is essential for improving the design of specific and potent inhibitors. Herein, we explored fast 19F- and 1H-detected magic angle spinning NMR spectroscopy to investigate the interaction between two fluorinated ligand diastereomers with the microcrystalline galectin-3 carbohydrate recognition domain. The detailed environment around the fluorine atoms was mapped by 2D 13C-19F and 1H-19F dipolar correlation experiments and permitted characterization of the binding interface. Our results demonstrate that 19F MAS NMR is a powerful tool for detailed characterization of protein-ligand interfaces and protein interactions at the atomic level.

The effect of the Solar System Ephemeris on the search for the nano-Hz gravitational wave background

ABSTRACT The detection of the nano-Hz gravitational-wave background (GWB) is one of the main targets of Pulsar timing arrays (PTAs). The detection can be achieved via searching for a common signal with quadrapolar correlation between pulsar pairs. Errors in the Solar-System ephemeris (SSE) can induce dipolar correlations in PTA data, which may affect the results of GWB searches, especially when the data quality is not high enough to constrain the correlation pattern. We investigate the effect of unmodelled SSE errors on GWB searches with PTAs, using simulations with properties based on the European Pulsar Timing Array data set. When the GWB signal is strong, SSE errors have little effect on the GWB search results, including parameter inference and model selection. When the GWB signal is weak, SSE errors can lead to overestimation of the GWB amplitude. However, model comparison would show strong support for dipolar correction, which implies the source of the common signal to be SSE-related and helps avoid its misidentification as a GWB signal. This indicates that SSE error is unlikely to be the main source of the common signal detected recently with real PTA data. We also use simulations to test the ability of the SSE model LINIMOSS in absorbing SSE-error signals and leaving the GWB signal intact. We show that marginalizing LINIMOSS planetary parameters with infinite priors is good at absorbing SSE errors, but may also lead to improper absorption of a GWB signal. Caution is therefore required when setting appropriate limits on the priors of SSE parameters.

Deep-Learning Interatomic Potential Connects Molecular Structural Ordering to the Macroscale Properties of Polyacrylonitrile.

Polyacrylonitrile (PAN) is an important commercial polymer, bearing atactic stereochemistry resulting from nonselective radical polymerization. As such, an accurate, fundamental understanding of governing interactions among PAN molecular units is indispensable for advancing the design principles of final products at reduced processability costs. While ab initio molecular dynamics (AIMD) simulations can provide the necessary accuracy for treating key interactions in polar polymers, such as dipole-dipole interactions and hydrogen bonding, and analyzing their influence on the molecular orientation, their implementation is limited to small molecules only. Herein, we show that the neural network interatomic potentials (NNIPs) that are trained on the small-scale AIMD data (acquired for oligomers) can be efficiently employed to examine the structures and properties at large scales (polymers). NNIP provides critical insight into intra- and interchain hydrogen-bonding and dipolar correlations and accurately predicts the amorphous bulk PAN structure validated by modeling the experimental X-ray structure factor. Furthermore, the NNIP-predicted PAN properties, such as density and elastic modulus, are in good agreement with their experimental values. Overall, the trend in the elastic modulus is found to correlate strongly with the PAN structural orientations encoded in the Hermans orientation factor. This study enables the ability to predict the structure-property relations for PAN and analogues with sustainable ab initio accuracy across scales.

Fractonic quantum quench in dipole-constrained bosons

We investigate the quench dynamics in the dipolar Bose-Hubbard model (DBHM) in one dimension. The boson hopping is constrained by dipole conservation and shows fractonic dynamics. The ground states at large Hubbard interaction U are Mott insulators at integer filling and a period-2 charge density wave (CDW) at half-integer filling. We focus on Mott-to-Mott and CDW-to-CDW quenches and find that dipole correlation spreading shows the light-cone behavior with the Lieb-Robinson (LR) velocity proportional to the dipole kinetic energy J and the square of the density in the case of Mott quench at integer filling. An effective model for postquench dynamics is constructed under the dilute-dipole approximation and fits the numerical results well. For the CDW quench, we observe a much reduced LR velocity of order J2/U and additional periodic features in the time direction. The emergence of a CDW ground state and the reduced LR velocity at half-integer filling can both be understood by careful application of the second-order perturbation theory. The oscillatory behavior arises from quantum scars in the quadrupole sector of the spectrum and is captured by a PXP-like model that we derive by projecting the DBHM to the quadrupolar sector of the Hilbert space. Published by the American Physical Society 2024

Water structural effects on DNA–DNA interactions and homologous recognition

Comprehending the principles underlying the interaction between DNA molecules in electrolyte solution is of crucial importance for understanding the phenomena of DNA condensation, recognition of homologous genes, and properties of DNA liquid crystals. Although DNA was considered in all its helical complexity over the last two decades, only a primitive, local, electrostatic model of the aqueous solution was considered. The forces acting between DNA molecules however must be influenced by the structure of the liquid separating them. In this paper we make a step towards unravelling earlier neglected effects of water structure on DNA–DNA interactions. We develop a model of DNA interaction accounting for the nonlocal dielectric response of water and of the electrolyte plasma dissolved in it. We focus particularly on the study of the dipolar overscreening effect, which leads to decaying oscillations of the electrostatic potential about DNA, and how it will affect electrostatic energy surfaces as a function of interaxial separation and mutual azimuthal orientation of the parallelly aligned interacting DNAs. We found that going beyond the classical electrostatic description of water (the so-called primitive model) reveals a complex oscillatory interaction surface in space, with many possible metastable configurations. These however vanish rapidly with smearing of the DNA charge distribution, due to dephasing of the oscillatory components of the interaction. This dephasing results in the suppression of oscillation amplitudes and leads to the dominance of non-oscillatory components in spatial dipolar correlations and the Debye screening. These dominant correlation patterns are shown to lead to a substantial enhancement of the difference between the interaction of homologous and nonhomologous DNA sequences, deepening and sharpening the homology recognition well.

Comparative Study of the Optical and Dielectric Anisotropy of a Difluoroterphenyl Dimer and Trimer Forming Two Nematic Phases.

We present a comparative study of the optical and dielectric anisotropy of a laterally fluorinated liquid crystal dimer and its homologous trimer, both exhibiting two nematic phases. In the high-temperature nematic phase, both oligomers exhibit positive optical anisotropy with similar magnitude, which, however, is lower in comparison with the optical anisotropy of the monomer. In the same temperature range, the dielectric permittivity along and perpendicular to the nematic director, measured on magnetically aligned samples, reveals negative dielectric anisotropy for both oligomers, which saturates as the temperature approaches the N-N phase transition temperature. Comparison of the dielectric anisotropies of the oligomers with the corresponding anisotropy of the monomer indicates a systematic variation of its magnitude with the number of the linked mesogenic units. Results are compared with the corresponding anisotropies of the cyanobiphenyl dimers, the archetypal compounds with two nematic phases, and are discussed in terms of the dipolar structure of the mesogens and the dipolar correlations in their nematic phases.

Linear and Nonlinear Dielectric Response of Intrinsically Disordered Proteins.

Linear and nonlinear dielectric responses of solutions of intrinsically disordered proteins (IDPs) were analyzed by combining molecular dynamics simulations with formal theories. A large increment of the linear dielectric function over that of the solvent is found and related to large dipole moments of IDPs. The nonlinear dielectric effect (NDE) of the IDP far exceeds that of the bulk electrolyte, offering a route to interrogate protein conformational and rotational statistics and dynamics. Conformational flexibility of the IDP makes the dipole moment statistics consistent with the gamma/log-normal distributions and contributes to the NDE through the dipole moment's non-Gaussian parameter. The intrinsic non-Gaussian parameter of the dipole moment combines with the protein osmotic compressibility in the nonlinear dielectric susceptibility when dipolar correlations are screened by the electrolyte. The NDE is dominated by dipolar correlations when electrolyte screening is reduced.

Thermodynamic information geometry of criticality, fluctuation anomaly and hyperscaling breakdown in the spin-3/2 chain

Equilibrium state space geometry is worked out for the exactly solved one-dimensional spin-3/2 lattice with a Blume–Emery–Griffiths (BEG) Hamiltonian as well as a more general one with a non-zero field coupled to the octopole moments. The phase behaviour of the spin-3/2 chain is revisited and novel observations of anomaly in the hyperscaling relation and in the decay of fluctuations are reported for the first time. Using the method of constrained fluctuations developed earlier in Sahay (2017); Sanwari and Sahay (2022) three appropriate state space sectional curvatures and a 3d curvature are shown to separately encode dipolar, quadrupolar and octopolar correlations both near and away from pseudo-criticality. In all observations of hyperscaling breakdown the 3d scalar curvature is found to encode the correlation length while the relevant sectional curvature equals the inverse of singular free energy. For parameter values where the order parameter fluctuation anomalously decays despite a divergence in its correlation length the relevant scalar curvature undergoes a sign change to positive values, signalling a possible change in the nature of the underlying statistical interactions.

Observing gravitational waves with solar system astrometry

The subtle influence of gravitational waves on the apparent positioning of celestial bodies offers novel observational windows [1,2,3,4]. We calculate the expected astrometric signal induced by an isotropic Stochastic Gravitational Wave Background (SGWB) in the short distance limit. Our focus is on the resultant proper motion of Solar System objects, a signal on the same time scales addressed by Pulsar Timing Arrays (PTA). We derive the corresponding astrometric deflection patterns, finding that they manifest as distinctive dipole and quadrupole correlations or, in some cases, may not be present. Our analysis encompasses both Einsteinian and non-Einsteinian polarisations. We estimate the upper limits for the amplitude of SGWBs that could be obtained by tracking the proper motions of large numbers of solar system objects such as asteroids. We find that for SGWBs with negative spectral indices, such as that generated by Super Massive Black Hole Binaries (SMBHB), the constraints from these observations could rival those from PTAs. With the Gaia satellite and the Vera C. Rubin Observatory poised to track an extensive sample of asteroids — ranging from 𝒪(105) to 𝒪(106), we highlight the significant future potential for similar surveys to contribute to our understanding of the SGWB.

Cooperative states and shift in resonant scattering of an atomic ensemble

We investigate the spectral shift known as the collective Lamb shift in forward scattering for a cold dense atomic cloud. The shift results from resonant dipole–dipole interaction mediated by real and virtual photon exchange, forming many-body states displaying various super- and subradiant behaviour. However, the scattering spectrum reflects the overall contributions from these states but also averages out the radiative details associated with the underlying spin orders, causing ambiguity in determination and raising controversy on the scaling property of this shift. We employ a Monte–Carlo simulation to study how the collective states contribute to emission. We thus distinguish two kinds of collective shift that follow different scaling laws. One results from dominant occupation of the near-resonant collective states. This shift is usually small and insensitive to the density or the number of participating atoms. The other comes from large spatial correlation of dipoles, associated with the states of higher degree of emission. This corresponds to larger collective shift that is approximately linearly dependent on the optical depth. We further demonstrate that the spatial spin order plays an essential role in superradiant emission. Our analysis provides a novel perspective for understanding collective scattering and cooperative effects.

A-site cation controlled localization of dipole correlations in a relaxor material

A-site cation controlled localization of dipole correlations in a relaxor material

Triclinic La7Zn2P11 with P3-, P24-, and P35- units: a combined study by 31P solid-state NMR spectroscopy and single crystal X-ray diffraction.

The ternary polyphosphide La7Zn2P11 was synthesized from the elements by using a salt flux or via a ceramic method in sealed quartz ampoules. The obtained samples were investigated by X-ray powder and single crystal diffraction: own type, P1̄, a = 775.33(13), b = 827.45(13), c = 1502.8(3) pm, α = 82.111(3), β = 77.034(3), γ = 89.996(3)°, wR2 = 0.1553, 5852 F2 values and 183 variables. This peculiar structure is characterized by the simultaneous presence of three distinct anionic phosphide species, namely P3-, P24-, and P35- units. La7Zn2P11 is an electron precise Zintl phase: (7La3+)21+(2Zn2+)4+(4P3-)12-(2P24-)8-(P35-). The P-P single bond distances range from 219.2 to 223.0 pm. The zinc sites show tetrahedral phosphorus coordination by three P3- and one P24- species. The tetrahedra are condensed to chains via common corners. The P35- units with P-P-P angles of 113.7° have exclusively lanthanum coordination. 31P solid-state NMR was used to probe the phosphorus local environments, connectivities and spatial proximities. The eleven crystallographically distinct phosphorus atoms were assigned with the help of two-dimensional homonuclear dipolar correlation experiments. Even though the application of 2D measurements on such phosphorus-based polyanionic compounds is exceedingly challenging because of the wide dispersion of chemical shifts, the fast irreversible decay of the transverse magnetization, and slow spin-lattice relaxation, a complete assignment is possible using radiofrequency-driven dipolar recoupling (RFDR), J-RESOLVED and total-through-bond correlation with R-sequence (R-TOBSY) techniques.

The Debye's model for the dielectric relaxation of liquid water and the role of cross-dipolar correlations. A MD-simulations study.

By means of massive (more than 1.2 · 106 molecules) molecular dynamics simulations at 300K we have disentangled self- and cross-dipolar contributions to the dielectric relaxation of liquid water that cannot be experimentally resolved. We have demonstrated that cross dipolar correlations are of paramount importance. They amount for almost a 60% of the total dielectric amplitude. The corresponding relaxation function is a one-step Debye-like function with a characteristic time, τcross, of the order of the phenomenological Debye time, τD. In contrast, the relaxation function corresponding to the self-contribution is rather complex and contains a fast decay related to dipolar librations and a second relaxation step that can be well described by two exponentials: a low-amplitude fast process (τ0 = 0.31ps) and a main slow process (τself = 5.4ps) that fully randomizes the dipolar orientation. In addition to dipolar relaxation functions, we have also calculated scattering-like magnitudes characterizing translation and rotation of water molecules. Although these processes can be considered as "jump" processes in the short time range, at the time scale of about τD-τcross, at which the cross-dipolar correlations decay to zero, the observed behavior cannot be distinguished from that corresponding to uncoupled Brownian translational and rotational diffusion. We propose that this is the reason why the Debye model, which does not consider intermolecular dipolar interactions, seems to work at time t ≳ τD.

Why Dissolving Salt in Water Decreases Its Dielectric Permittivity.

The dielectric permittivity of salt water decreases on dissolving more salt. For nearly a century, this phenomenon has been explained by invoking saturation in the dielectric response of the solvent water molecules. Herein, we employ an advanced deep neural network (DNN), built using data from density functional theory, to study the dielectric permittivity of sodium chloride solutions. Notably, the decrease in the dielectric permittivity as a function of concentration, computed using the DNN approach, agrees well with experiments. Detailed analysis of the computations reveals that the dominant effect, caused by the intrusion of ionic hydration shells into the solvent hydrogen-bond network, is the disruption of dipolar correlations among water molecules. Accordingly, the observed decrease in the dielectric permittivity is mostly due to increasing suppression of the collective response of solvent waters.