Line-broadening Effects Research Articles

Temperature-Dependent Line-Broadening Effects in CO2 Caused by Ar.

This computational study of line-broadening effects is based on an accurate, analytical representation of the intermonomer potential energy surface (PES) of the CO2 ⋅ Ar van der Waals (vdW) complex. The PES is employed to compute collisional broadening coefficients for rovibrational lines of CO2 perturbed by Ar. The semiclassical computations are performed using the modified Robert-Bonamy approach, including real and imaginary terms, and the exact trajectory model. The lines investigated are in the 10001←00011, 01101←00001, 00011←00001, and 00031←00001 vibrational bands and the computations are repeated at multiple temperatures. The computed results are in good agreement with the available experimental values, validating both the intermonomer PES developed and the methodology used. For lines in the 01101←00001 band of CO2 , temperature-dependent Ar-broadening coefficients are reported for the first time. The parameters presented should prove useful, among other applications, for the accurate experimental determination of CO2 and Ar abundances in planetary atmospheres.

Spectroscopically dark phosphate features revealed by chemical exchange saturation transfer.

Phosphate is an essential anion in the human body, comprising approximately 1% of the total body weight, and playing a vital role in metabolism, cell membranes, and bone formation. We have recently provided spectroscopic, microscopic, and computational evidence indicating that phosphates can aggregate much more readily in solution than previously thought. This prior work provided indirect evidence through the observation of unusual P NMR relaxation and line-broadening effects with increasing temperature. Here, we show that, under conditions of slow exchange and selective RF saturation, additional features become visible in chemical exchange saturation transfer (CEST) experiments, which appear to be related to the previously reported phosphate clustering. In particular, CEST shows pronounced dips several ppm upfield of the main phosphate resonance at low temperatures, while direct P spectroscopy does not produce any signals in that range. We study the pH dependence of these new spectroscopic features and present exchange and spectroscopic parameters based on fitting the CEST data. These findings could be of importance in the investigation of phosphate dynamics, especially in the biological milieu.

Current limitations of solid-state NMR in carbohydrate and cell wall research

High-resolution investigation of cell wall materials has emerged as an important application of biomolecular solid-state NMR (ssNMR). Multidimensional correlation experiments have become a standard method for obtaining sufficient spectral resolution to determine the polymorphic structure of carbohydrates and address biochemical questions regarding the supramolecular organization of cell walls. Using plant cellulose and matrix polysaccharides as examples, we will review how the multifaceted complexity of polysaccharide structure is impeding the resonance assignment process and assess the available biochemical and spectroscopic approaches that could circumvent this barrier. We will emphasize the ineffectiveness of the current methods in reconciling the ever-growing dataset and deriving structural information. We will evaluate the protocols for achieving efficient and homogeneous hyperpolarization across the cell wall material using magic-angle spinning dynamic nuclear polarization (MAS-DNP). Critical questions regarding the line-broadening effects of cell wall molecules at cryogenic temperature and by paramagnetic biradicals will be considered. Finally, the MAS-DNP method will be placed into a broader context with other structural characterization techniques, such as cryo-electron microscopy, to advance ssNMR research in carbohydrate and cell wall biomaterials.

Evaluation strategy towards an accurate determination of viscosity and interfacial tension by surface light scattering in presence of line-broadening effects

HypothesisThe accurate determination of viscosity and interfacial tension by surface light scattering (SLS) represents a challenging task, especially in the range of small wave vectors. Here, measurements are subjected to line-broadening effects, which are often not adequately described by empirical fitting routines in literature. ExperimentsFor tackling this limitation, a novel evaluation strategy relying on a Monte-Carlo-based optimization is suggested in the present study. Without making prior assumptions about the underlying distribution of wave vectors, the method allows to decompose the measured SLS signal into a superposition of individual contributions represented by damped oscillations. The resulting amplitude distribution for damping and frequency is used to estimate the central wave vector, all of which is required to solve the dispersion relation for hydrodynamic surface fluctuations in its exact form. FindingsBy applying the evaluation strategy to SLS signals recorded in reflection direction for the reference fluid toluene, it is demonstrated that the presented concept provides a route towards an accurate determination of viscosity and surface tension in the range of small wave vectors. Hence, the strategy is considered to extend the application range of SLS in connection with opaque and non-transparent fluids for which small wave vectors often need to be probed experimentally.

Molecular Dynamics-Assisted Optimization of Protein NMR Relaxation Analysis.

NMR relaxation analysis of the mobile residues in globular proteins is sensitive to the form of the experimentally fitted internal autocorrelation function, which is used to represent that motion. Different order parameter representations can precisely fit the same set of 15N R1, R2, and heteronuclear NOE measurements while yielding significantly divergent predictions of the underlying autocorrelation functions, indicating the insufficiency of these experimental relaxation data for assessing which order parameter representation provides the most physically realistic predictions. Molecular dynamics simulations offer an unparalleled capability for discriminating among different order parameter representations to assess which representation can most accurately model a wide range of physically realistic autocorrelation functions. Six currently utilized AMBER and CHARMM force fields were applied to calculate autocorrelation functions for the backbone H–N bond vectors of ubiquitin as an operational test set. An optimized time constant-constrained triexponential (TCCT) representation was shown to markedly outperform the widely used (Sf2,τs,S2) extended Lipari–Szabo representation and the more closely related (Sf2,SH2, SN2) Larmor frequency-selective representation. Optimization of the TCCT representation at both 600 and 900 MHz 1H converged to the same parameterization. The higher magnetic field yielded systematically larger deviations in the back-prediction of the autocorrelation functions for the mobile amides, indicating little added benefit from multiple field measurements in analyzing amides that lack slower (∼ms) exchange line-broadening effects. Experimental 15N relaxation data efficiently distinguished among the different force fields with regard to their prediction of ubiquitin backbone conformational dynamics in the ps–ns time frame. While the earlier AMBER 99SB and CHARMM27 force fields underestimate the scale of backbone dynamics, which occur in this time frame, AMBER 14SB provided the most consistent predictions for the well-averaged highly mobile C-terminal residues of ubiquitin.

Surface light scattering in reflection geometry: capabilities and limitations.

In the present study, the capabilities and limitations of surface light scattering (SLS) experiments in reflection geometry are investigated. Based on the study of the transparent reference fluid toluene at 303.15 K over a wide range of wave vectors between (0.3and6.6)×105m-1, the performance of two different detection schemes analyzing light scattered from the vapor-liquid interface in a perpendicular and non-perpendicular direction is assessed. Considering various aspects such as the quality of the heterodyne correlation functions, the input information for data evaluation, and the line-broadening effects, both detection schemes show comparable overall efficiency. For wave vectors larger than 4.5×105m-1, where line-broadening effects are suppressed, the results obtained for liquid viscosity and surface tension agree with measurements in transmission geometry, validating the capability of the apparatus. For wave vectors smaller than 1.5×105m-1, the SLS signals are distinctly affected by line-broadening effects, which will result in erroneous values for surface tension and in particular viscosity, even if empirical fitting approaches commonly used in literature are applied. The modeling of the influence of line broadening on the measurements results by a simple Gaussian-weighted sum of individual damped oscillations reveals the increasing complexity of the underlying wave vector distribution toward smaller wave vectors chosen for the scattering geometry.

Carbonyl 13C-detect solution-state protein NMR experiments to circumvent amide-solvent exchange broadening: Application to β2-microglobulin

The 15N–1H heteronuclear single-quantum correlation (HSQC) technique in protein NMR spectroscopy suffers from line-broadening effects, such as chemical exchange of labile protons with solvent, and exchange broadening for residues undergoing conformational dynamics.The amide resonance of β2-microglobulin residue S88 is not observed in the HSQC spectrum but can be obtained through 13C-detect experiments that circumvent the problem of amide-solvent exchange broadening.Line broadening of S88 resonance beyond detection in the HSQC spectrum is not attributed to conformational exchange but rather to solvent exchange occurring on the order of ~103 s−1.

Exploiting line-mixing effects for laser absorption spectroscopy at extreme combustion pressures

A unique spectroscopic strategy has been developed for laser absorption sensing of carbon monoxide (CO) and carbon dioxide (CO2) at extreme pressures (P > 50 atm) relevant to modern combustion devices. The strategy exploits the band narrowing effects of line mixing, which acutely impact spectrally dense regions, such as bandheads, where line spacing is small. Line mixing is shown to counter collisional line-broadening effects that reduce differential absorption at elevated pressures and often limit the pressure range of laser absorption methods. In this work, the R-branch bandheads of CO and CO2, which are only observed at high temperatures relevant to combustion, are targeted near 2.3 µm and 4.2 µm, respectively. Spectral line-mixing models were developed for each bandhead region to account for the collision-induced population transfer rates between rotational energy states over a wide range of elevated temperatures and pressures. Modified-exponential-gap models using the relaxation matrix formalism were shown to capture the thermodynamic dependence of the population transfer rates and enabled scaling. Differential absorption at the bandheads was observed to increase by up to a factor of ten at high gas densities, due to line-mixing effects, enabling detection with relatively narrow-band tunable semi-conductor lasers. With refined spectroscopic models, laser absorption measurements of temperature, CO, and CO2 were demonstrated over a range of high pressures (up to 104 atm) in a sub-scale rocket combustor operated with kerosene and supercritical methane.

Mapping of fatty acid composition with free-breathing MR spectroscopic imaging and compressed sensing.

Nonalcoholic fatty liver disease (NAFLD) is a growing health problem, and a major challenge in NAFLD management is identifying which patients are at risk of progression to more serious disease. Simple measurements of liver fat content are not strong predictors of clinical outcome, but biomarkers related to fatty acid composition (ie, saturated vs. unsaturated fat) may be more effective. MR spectroscopic imaging (MRSI) methods allow spatially resolved, whole‐liver measurements of chemical composition but are traditionally limited by slow acquisition times. In this work we present an accelerated MRSI acquisition based on spin echo single point imaging (SE‐SPI), which, using appropriate sampling and compressed sensing reconstruction, allows free‐breathing acquisition in a mouse model of fatty liver disease. After validating the technique's performance in oil/water phantoms, we imaged mice that had received a normal diet or a methionine and choline deficient (MCD) diet, some of which also received supplemental injections of iron to mimic hepatic iron overload. SE‐SPI was more resistant to the line‐broadening effects of iron than single‐voxel spectroscopy measurements, and was consistently able to measure the amplitudes of low‐intensity spectral peaks that are important to characterizing fatty acid composition. In particular, in the mice receiving the MCD diet, SE‐SPI showed a significant decrease in a metric associated with unsaturated fat, which is consistent with the literature. This or other related metrics may therefore offer more a specific biomarker of liver health than fat content alone. This preclinical study is an important precursor to clinical testing of the proposed method.MR‐based quantification of fatty acid composition may allow for improved characterization of non‐alcoholic fatty liver disease. A spectroscopic imaging method with appropriate sampling strategy allows whole‐liver mapping of fat composition metrics in a free‐breathing mouse model. Changes in metrics like the surrogate unsaturation index (UIs) are visible in mice receiving a diet which induces fat accumulation in the liver, as compared to a normal diet; such metrics may prove useful in future clinical studies of liver disease.

57Fe Mössbauer study of high-yield CuFe2O4 nanoparticles produced by the levitation-jet aerosol technique with post-synthesis annealing

Pseudo-spherical cubic-shaped nanoparticles of spinel ferrite CuFe2O4 have been prepared using a two-stage process. At first, an evaporation of levitating copper–iron drop into mix of helium–air gas flow took place, which resulting in copper ferrite-based powders. Then, such powders were additionally oxidized trough the heterogeneous auto-wave combustion in open air. We studied the effect of performing the synthesis in either an air or a helium environment on the phase composition of nanoparticles, and how the use of a post-synthesis annealing step modifies this, using room temperature 57Fe Mossbauer spectroscopy. By applying this technique, we are able to distinguish between the normal (non-magnetic) and inverse cubic (magnetic) phases of CuFe2O4, which is usually inaccessible using X-ray diffraction, as well as quantifying their relative amounts within each sample. Furthermore, we have been able to quantify trace amounts of the tetragonal CuFe2O4, phases that are typically obscured by line-broadening effects within our X-ray diffraction data, which indicates that annealing using a propane flame can also cause a cubic to tetragonal distortion in the crystal structure of the spinel lattice. Finally, by combining our Mossbauer parameters, which are sensitive to the Fe-containing phases only, with X-ray diffraction data, which are sensitive to all phases, we report on the full phase composition for the first time for nanoparticles produced via this synthesis route.

Enabling High Spectral Resolution of Liquid Mixtures in Porous Media by Antidiagonal Projections of Two-Dimensional 1H NMR COSY Spectra.

The noninvasive, in situ chemical identification of liquid mixtures confined in porous materials is experimentally challenging. NMR is chemically resolved and applicable to optically opaque systems but suffers from a significant loss in spectral resolution in the presence of the magnetic field inhomogeneities typical of porous media. In this work, we introduce a method of analysis of conventional two-dimensional (2D) 1H NMR correlation spectroscopy (COSY) spectra based on the extraction of 1D antidiagonal projections, which are free from line-broadening effects and can therefore be used for chemical species identification. Here, we show the application of the technique to the measurement of linear n-alkanes where the cross-to-diagonal peak ratios are shown to follow a power-law curve as a function of the chain length. This calibration enables quantifying mixtures of linear hydrocarbons confined in any porous material independently of temperature or inter-molecular dynamics. Thus, this is a promising tool for quantitative chemical reaction monitoring studies in heterogeneous systems under operando experimental conditions.

Line-broadening and anharmonic effects in the attenuated total reflectance infrared spectra of calcite

Line-broadening and anharmonic effects in the attenuated total reflectance infrared spectra of calcite

Allosteres to regulate neurotransmitter sulfonation

Catecholamine neurotransmitter levels in the synapses of the brain shape human disposition-cognitive flexibility, aggression, depression, and reward seeking-and manipulating these levels is a major objective of the pharmaceutical industry. Certain neurotransmitters are extensively sulfonated and inactivated by human sulfotransferase 1A3 (SULT1A3). To our knowledge, sulfonation as a therapeutic means of regulating transmitter activity has not been explored. Here, we describe the discovery of a SULT1A3 allosteric site that can be used to inhibit the enzyme. The structure of the new site is determined using spin-label-triangulation NMR. The site forms a cleft at the edge of a conserved ∼30-residue active-site cap that must open and close during the catalytic cycle. Allosteres anchor into the site via π-stacking interactions with two residues that sandwich the planar core of the allostere and inhibit the enzyme through cap-stabilizing interactions with substituents attached to the core. Changes in cap free energy were calculated ab initio as a function of core substituents and used to design and synthesize a series of inhibitors intended to progressively stabilize the cap and slow turnover. The inhibitors bound tightly (34 nm to 7.4 μm) and exhibited progressive inhibition. The cap-stabilizing effects of the inhibitors were experimentally determined and agreed remarkably well with the theoretical predictions. These studies establish a reliable heuristic for the design of SULT1A3 allosteric inhibitors and demonstrate that the free-energy changes of a small, dynamic loop that is critical for SULT substrate selection and turnover can be calculated accurately.

Electron heating and thermal relaxation of gold nanorods revealed by two-dimensional electronic spectroscopy

To elucidate the complex interplay between the size and shape of gold nanorods and their electronic, photothermal, and optical properties for molecular imaging, photothermal therapy, and optoelectronic devices, it is a prerequisite to characterize ultrafast electron dynamics in gold nanorods. Time-resolved transient absorption (TA) studies of plasmonic electrons in various nanostructures have revealed the time scales for electron heating, lattice vibrational excitation, and phonon relaxation processes in condensed phases. However, because linear spectroscopic and time-resolved TA signals are vulnerable to inhomogeneous line-broadening, pure dephasing and direct electron heating effects are difficult to observe. Here we show that femtosecond two-dimensional electronic spectroscopy, with its unprecedented time resolution and phase sensitivity, can be used to collect direct experimental evidence for ultrafast electron heating, anomalously strong coherent and transient electronic plasmonic responses, and homogenous dephasing processes resulting from electron-vibration couplings even for polydisperse gold nanorods.

Ultra-sensitive probe of spectral line structure and detection of isotopic oxygen

We discuss a new method of investigating and obtaining quantitative behavior of higher harmonic (> 2f) wavelength modulation spectroscopy (WMS) based on the signal structure. It is shown that the spectral structure of higher harmonic WMS signals, quantified by the number of zero crossings and turnings points, can have increased sensitivity to ambient conditions or line-broadening effects from changes in temperature, pressure, or optical depth. The structure of WMS signals, characterized by combinations of signal magnitude and spectral locations of turning points and zero crossings, provides a unique scale that quantifies lineshape parameters and, thus, useful in optimization of measurements obtained from multi-harmonic WMS signals. We demonstrate this by detecting weaker rotational–vibrational transitions of isotopic atmospheric oxygen (16O18O) in the near-infrared region where higher harmonic WMS signals are more sensitive contrary to their signal-to-noise ratio considerations. The proposed approach based on spectral structure provides the ability to investigate and quantify signals not only at linecenter but also in the wing region of the absorption profile. This formulation is particularly useful in tunable diode laser spectroscopy and ultra-precision laser-based sensors where absorption signal profile carries information of quantities of interest, e.g., concentration, velocity, or gas collision dynamics, etc.

Nitroxide Labeling of Proteins and the Determination of Paramagnetic Relaxation Derived Distance Restraints for NMR Studies.

Site-specific attachment of paramagnetic spin labels to biomolecules causes distance-dependent line-broadening effects, which can be exploited to study the structure and dynamics of these molecules in solution. This protocol describes how to attach nitroxide spin labels to proteins and how to collect and analyze NMR data using these labeled samples. We also explain how to derive distance restraints for paramagnetic relaxation enhancement nuclear magnetic resonance (PRE-NMR) studies.

Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin.

Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb.

A 2D proton J-resolved NMR method for direct measurements on heterogeneous foods

NMR spectroscopy is recognized as a powerful tool for food analyses on chemical composition determination, molecular structure elucidation, and functional component identification. Due to inhomogeneous line-broadening effects originating from sample heterogeneities and residual anisotropic interactions, high-resolution NMR available for analyses on heterogeneous food samples generally recurs to sample extraction and magic-angle spinning based measurements. In this study, we proposed an NMR approach for high-resolution 2D proton (1H) J-resolved measurements directly from heterogeneous foods without any sample pretreatment or additional hardware requirement. The noteworthy enhancement in spectral resolution and quality is illustrated in our experiments on two common heterogeneous food samples, a tomato and a fish. The resulting spectra yield a wealth of chemical shifts and J coupling information for analyses on an intact tomato pulp and a whole zebra fish. This method presents a complementary way to the conventional NMR methods for analyses on comparison, discrimination, and classification of heterogeneous foods. Furthermore, this method is applicable on common liquid-state NMR spectrometers since no additional hardware device is required, constituting a convenient and promising manner for practical applications to heterogeneous foods.

Paramagnetic Nanoparticles Leave Their Mark on Nuclear Spins of Transiently Adsorbed Proteins.

The successful application of nanomaterials in biosciences necessitates an in-depth understanding of how they interface with biomolecules. Transient associations of proteins with nanoparticles (NPs) are accessible by solution NMR spectroscopy, albeit with some limitations. The incorporation of paramagnetic centers into NPs offers new opportunities to explore bio-nano interfaces. We propose NMR paramagnetic relaxation enhancement as a new tool to detect NP-binding surfaces on proteins with increased sensitivity, also extending the applicability of NMR investigations to heterogeneous biomolecular mixtures. The adsorption of ubiquitin on gadolinium-doped fluoride-based NPs produced residue-specific NMR line-broadening effects mapping to a contiguous area on the surface of the protein. Importantly, an identical paramagnetic fingerprint was observed in the presence of a competing protein-protein association equilibrium, exemplifying possible interactions taking place in crowded biological media. The interaction was further characterized using isothermal titration calorimetry and upconversion emission measurements. The data indicate that the used fluoride-based NPs are not biologically inert but rather are capable of biomolecular recognition.

Reduced-density-matrix description for pump-probe optical phenomena in moving atomic systems

Linear and nonlinear (especially coherent) electromagnetic interactions of moving many-electron atoms are investigated using a reduced-density-matrix description, which is applied to electromagnetically induced transparency and related resonant pump-probe optical phenomena. External magnetic fields are included on an equal footing with the electromagnetic fields and spin-Zeeman interactions are taken into account. Complimentary time-domain (equation-of-motion) and frequency-domain (resolvent-operator) formulations of the reduced-density-matrix description are self-consistently developed. The general nonperturbative and non-Markovian formulations provide a fundamental framework for systematic evaluations of corrections to the standard Born (lowest-order-perturbation) and Markov (short-memory-time) approximations. The macroscopic electromagnetic response is described semiclassically, employing a perturbation expansion of the reduced-density operator in powers of the classical electromagnetic field. Our primary results are compact Liouville-space operator expressions for the linear and general ($n\text{th}$-order) nonlinear macroscopic electromagnetic-response tensors, which can be evaluated for nonlocal and nonstationary optical media described by multilevel atomic-system representations. Interactions among atoms and with environmental photons are treated as line-broadening effects by means of a general Liouville-space self-energy operator, for which the tetradic-matrix elements are explicitly evaluated in the diagonal, lowest-order, and Markov approximations. The compact Liouville-space operator expressions that are derived for the macroscopic electromagnetic-response tensors are introduced into the dynamical description of the electromagnetic-field propagation. It is pointed out that a quantized-electromagnetic-field approach will be required for a fully self-consistent quantum-mechanical treatment of local-field effects and radiative corrections.