Crowded Spectra Research Articles

Chemometric Classification of Motor Oils Using 1H NMR Spectroscopy With Simultaneous Phase and Baseline Optimization

ABSTRACTHere, we demonstrate mid‐field 1H NMR spectroscopy combined with chemometrics to be powerful in the classification and authentication of motor oils (MOs). The 1H NMR data were processed with a new algorithm for simultaneous phase and baseline correction, which, for crowded spectra such as those of the refinery products, allowed for more accurate estimation of phase parameters than other literature approaches tested. A principal component analysis (PCA) model based on the unbinned CH3 fingerprint region (0.6–1.0 ppm) enabled the differentiation of hydrocracked and poly‐α‐olefin‐based MOs and was effective in resolving mixtures of these base stocks with conventional base oils. PCA analysis of the 1.0‐ to 1.14‐ppm region enabled the detection of poly (isobutylene) additive and was useful for differentiating between single‐grade and multigrade MOs. Non‐equidistantly binned 1H NMR data were used to detect the addition of esters and to establish discriminant models for classifying MOs by viscosity grade and by major categories of synthetic, semisynthetic, and mineral oils. The performances of four classifiers (linear discriminant analysis [LDA], quadratic discriminant analysis [QDA], naïve Bayes classifier [NBC], and support vector machine [SVM]) with and without PCA dimensionality reduction were compared. In both tasks, SVM showed the best efficiency, with average error rates of ~2.3% and 8.15% for predicting major MO categories and viscosity grades, respectively. The potential to merge spectra collected from different NMR instruments is discussed for models based on spectral binning. It is also shown that small errors in phase parameters are not detrimental to binning‐based PCA models.

Detection of Tm ii Lines in the Spectra of Two s-process Rich Stars

Abstract Thulium abundance is unknown in the atmospheres of low and medium-mass evolved stars. The reason is the weakness of lines and the crowded spectra. We examined the spectra of two late-type stars in a broad wavelength region to search for thulium lines. Thulium abundance was estimated in the atmospheres of barium star HD 204075 and post-asymptotic giant branch star HD 235858 for the first time, log ϵ ( Tm ) ≃ 0.1 and ≲1.3, respectively.

Raw signal improvement using beam shaping plasma modulation for uranium detection in ore using laser-induced breakdown spectroscopy

Real-time quantitative detection of uranium in ores is one of the major challenges for uranium exploration. Laser-induced breakdown spectroscopy (LIBS) has been regarded as a most promising technique for this application. However, due to the matrix complexity as well as low uranium concentration of ore, the detection sensitivity of LIBS for uranium in ores is still unsatisfactory. This work explored the potential of a beam-shaping plasma modulation method to improve the limit of detection of uranium in ores. By shaping the profile of laser beam from normally Gaussian distribution to flat-top, the plasma was modulated to be more excited with reduced peak electron density at the laser-plasma interaction point for plasma shielding reduction especially at high laser energy as well as to be more morphologically stable for LIBS signal repeatability improvement. It was further found that this method enhanced LIBS signal intensity mainly by increasing the plasma temperature, while the electron density was almost unchanged, which was very attractive for uranium detection in ore since one of the major problem for uranium detection was that it is hard to find clear uranium spectral lines for analysis due to the high dense emission lines of ore samples in real cases and lower electron density, indicated less line broadening and less line overlap or interferences. A clear uranium emission line has been found in crowded ore spectra, and the intensity of U II 409.013 nm based on flat-top beam was about 5 times higher than that of Gaussian beam, and the relative standard deviation (RSD) of the signal was reduced by about 50%. Moreover, the LOD of uranium in ores was estimated to be 21.2 ppm with flat-top beam, indicating that beam shaping is a promising method for rapid and accurate detection of uranium in ores.

LLWP—A new Loomis-Wood software at the example of Acetone-13C1

Acetone-13C1 is a complex organic molecule with two internal methyl (-CH3) rotors having relatively low effective barriers to internal rotation of about 249cm−1. This leads to two low-lying torsional modes and five internal rotation components resulting in a dense and complicated spectrum. In this study, measurements of acetone-13C1 were performed with an isotopically enriched sample in the frequency range 37–1102GHz. Predicted spectra of acetone-13C1 created with ERHAM allow for future radio astronomical searches.Loomis-Wood plots are one approach to improve and fasten the analysis of such crowded spectra. In this study, the new Loomis-Wood software LLWP was used for fast and confident assignments. LLWP focuses on being user-friendly, intuitive, and applicable to a broad range of assignment tasks. The software is presented here and can be downloaded from llwp.astro.uni-koeln.de.

Fundamental and practical aspects of machine learning for the peak picking of biomolecular NMR spectra

Rapid progress in machine learning offers new opportunities for the automated analysis of multidimensional NMR spectra ranging from protein NMR to metabolomics applications. Most recently, it has been demonstrated how deep neural networks (DNN) designed for spectral peak picking are capable of deconvoluting highly crowded NMR spectra rivaling the facilities of human experts. Superior DNN-based peak picking is one of a series of critical steps during NMR spectral processing, analysis, and interpretation where machine learning is expected to have a major impact. In this perspective, we lay out some of the unique strengths as well as challenges of machine learning approaches in this new era of automated NMR spectral analysis. Such a discussion seems timely and should help define common goals for the NMR community, the sharing of software tools, standardization of protocols, and calibrate expectations. It will also help prepare for an NMR future where machine learning and artificial intelligence tools will be common place.

Ultrahigh-Resolution NMR with Water Signal Suppression for a Deeper Understanding of the Action of Antimetabolic Drugs on Diffuse Large B-Cell Lymphoma.

Ultrahigh-resolution NMR has recently attracted considerable attention in the field of complex samples analysis. Indeed, the implementation of broadband homonuclear decoupling techniques has allowed us to greatly simplify crowded 1H spectra, yielding singlets for almost every proton site from the analyzed molecules. Pure shift methods have notably shown to be particularly suitable for deciphering mixtures of metabolites in biological samples. Here, we have successfully implemented a new pure shift pulse sequence based on the PSYCHE method, which incorporates a block for solvent suppression that is suitable for metabolomics analysis. The resulting experiment allows us to record ultrahigh-resolution 1D NOESY 1H spectra of biofluids with suppression of the water signal, which is a crucial step for highlighting metabolite mixtures in an aqueous phase. We have successfully recorded pure shift spectra on extracellular media of diffuse large B-cell lymphoma (DLBCL) cells. Despite a lower sensitivity, the resolution of pure shift data was found to be better than that of the standard approach, which provides a more detailed vision of the exo-metabolome. The statistical analyses carried out on the resulting metabolic profiles allow us to successfully highlight several metabolic pathways affected by these drugs. Notably, we show that Kidrolase plays a major role in the metabolic pathways of this DLBCL cell line.

Spectral editing of alanine, serine, and threonine in uniformly labeled proteins based on frequency-selective homonuclear recoupling in solid-state NMR.

Spectral editing is crucial to simplify the crowded solid-state NMR spectra of proteins. New techniques are introduced to edit 13C-13C correlations of uniformly labeled proteins under moderate magic-angle spinning (MAS), based on our recent frequency-selective homonuclear recoupling sequences [Zhang et al., J. Phys. Chem. Lett. 2020, 11, 8077-8083]. The signals of alanine, serine, or threonine residues are selected out by selective 13Cα-13Cβ double-quantum filtering (DQF). The 13Cα-13Cβ correlations of alanine residues are selectively established with efficiency up to ~ 1.8 times that by dipolar-assisted rotational resonance (DARR). The techniques are shown in 2D/3D NCCX experiments and applied to the uniformly 13C, 15N labeled Aquaporin Z (AqpZ) membrane protein, demonstrating their potential to simplify spectral analyses in biological solid-state NMR.

Resolving overlapped signals with automated FitNMR analytical peak modeling

Nuclear magnetic resonance (NMR) is a valuable tool for determining the structures of molecules and probing their dynamics. A longstanding problem facing both small-molecule and macromolecular NMR is overlapped signals in crowded spectra. To address this, we have developed a method that extracts peak features by fitting analytically derived models of NMR lineshapes. The approach takes into account the effects of truncation, apodization, and the resulting artifacts, while avoiding systematic errors that have affected other models. Even severely overlapped peaks, beyond the point of coalescence, can be distinguished in both simulated and experimental data. We show that the method can measure unresolved backbone scalar couplings directly from a 2D proton-nitrogen spectrum of a de novo designed mini protein. The algorithm is implemented in the FitNMR open-source R package and can be used to analyze nearly any type of single or multidimensional data from small molecules or biomolecules.

Fully Exploiting the Power of 2D NMR J-Resolved Spectroscopy.

Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical tool that enables one to study molecular properties and interactions. Homonuclear couplings provide valuable structural information but are often difficult to disentangle in crowded 1H NMR spectra where complex multiplets and signal overlap commonly exist. Multidimensional NMR experiments push the power of NMR to a new level by providing better signal dispersion. Among them, 2D J-resolved spectroscopy is widely used for multiplet analysis and the measurement of scalar coupling constants. Here, we present a new 2D J-resolved method, CASCADE, through which easier multiplet analysis and unambiguous measurement of specific coupling constants can be achieved at the same time, fully exploiting the power of 2D J-resolved spectroscopy. It is expected that this method may replace a conventional 2D J experiment in many cases, facilitating structural and configurational studies as well as chemical and biological analyses.

PE-SERF: A sensitivity-improved experiment to measure JHH in crowded spectra.

Aiming at facilitating the analysis of molecular structure, the gradient-encoded selective refocusing methods (G-SERF) and a great number of its variants for measuring proton-proton coupling constants have been proposed. However, the sensitivity is an issue in the 2D gradient-encoded experiments, because the signal intensity is determined by the slice thickness of the sample that depends on encoding gradient and the bandwidth of selective pulses which is limited by the smallest chemical shift difference of any two coupled protons. Here, we present a method dubbed PE-SERF (perfect echo selective refocusing) which can determine all JHH values involving a selected proton with improved sensitivity compared to original G-SERF experiment. The modules of perfect echo involving selective pulses and gradient-encoded selective refocusing are combined in the method, so that the unwanted J couplings arising from coupled spin pairs in the same sample slice would be nullified. In this way, instead of single proton, a pair of coupled protons is allowed to share a sample slice, and thus the slice thickness can be increased and the spectral sensitivity can be improved. The performance of the method is demonstrated by experiments on quinine and strychnine.

Ultra-Clean Pure Shift 1H-NMR applied to metabolomics profiling

Even though Pure Shift NMR methods have conveniently been used in the assessment of crowded spectra, they are not commonly applied to the analysis of metabolomics data. This paper exploits the recently published SAPPHIRE-PSYCHE methodology in the context of plant metabolome. We compare single pulse, PSYCHE, and SAPPHIRE-PSYCHE spectra obtained from aqueous extracts of Physalis peruviana fruits. STOCSY analysis with simplified SAPPHIRE-PSYCHE spectra of six types of Cape gooseberry was carried out and the results attained compared with classical STOCSY data. PLS coefficients analysis combined with 1D-STOCSY was performed in an effort to simplify biomarker identification. Several of the most compromised proton NMR signals associated with critical constituents of the plant mixture, such as amino acids, organic acids, and sugars, were more cleanly depicted and their inter and intra correlation better reveled by the Pure Shift methods. The simplified data allowed the identification of glutamic acid, a metabolite not observed in previous studies of Cape gooseberry due to heavy overlap of its NMR signals. Overall, the results attained indicated that Ultra-Clean Pure Shift spectra increase the performance of metabolomics data analysis such as STOCSY and multivariate coefficients analysis, and therefore represent a feasible and convenient additional tool available to metabolomics.

Nonuniform Sampling for NMR Spectroscopy.

Nonuniform sampling was first proposed more than 40 years ago as an alternate method for sampling two-dimensional NMR data was initially pursued by only a small number of scientists. However, it has been gradually adopted after it was shown that major gains in measuring time and spectrum resolution can be obtained. Furthermore, migration of NMR software to the Unix environment facilitated development of new processing tools, and there is now a selection of programs available that yield high-quality reconstructions of NUS data. Moreover, it became obvious that recording high-resolution 3D and 4D protein NMR spectra at the resolution provided by modern high-field instruments was not possible with uniform sampling. It has become apparent that sparse, low dynamic-range NMR spectra, in particular, the triple resonance experiments are all best recorded with NUS. Optimal sampling schedules can yield benefits with respect to detecting weak peaks in high dynamic-range spectra and therefore a careful use of 2D HSQC-like spectra of mixed concentrations of small molecules is feasible. It is not yet clear whether crowded high dynamic-range spectra, such as NOESYs with many cross-peaks, benefit from NUS. On the other hand, NUS appears to be the best option for recording such high dynamic-range spectra if crowding can be reduced by shorten NOESY mixing times and/or by reducing overlap through isotopic labeling in high-resolution 3D and 4D experiments. Here we discuss principals and applications of the method, trying to provide a wide overview, but are biased by our own approaches. Thus, we will obviously miss important developments elsewhere and do not claim to be comprehensive.

Combining pure shift and J-edited spectroscopies: A strategy for extracting chemical shifts and scalar couplings from highly crowded proton spectra of oligomeric saccharides.

We report the application of pure shift and J-edited nuclear magnetic resonance spectroscopies to the structural analysis of a protected maltotrioside synthetic intermediate whose crowded 1 H spectrum displays highly crowded regions. The analytical strategy is based on the implementation of J-edited and TOCSY experiments whose resolution is optimized by the use of broadband homonuclear decoupling and selective refocusing techniques, to assign and measure chemical shifts and homonuclear scalar couplings with high accuracy. The resulting data show a high level of complementarity, providing a detailed insight into each subunit of this oligomeric saccharide, even for proton sites whose nuclear magnetic resonance signals strongly overlap. This approach allowed for fully assigning proton chemical shifts and extracting 80% of the 3 JHH couplings that are in excellent agreement with those expected for D-gluco-pyranosyl units in 4 C1 conformations.

Applications of Modulation Excitation Spectroscopy in Heterogeneous Catalysis

In situ and operando spectroscopic techniques are crucial for our understanding of complex heterogeneously catalyzed reactions. Under actual reaction conditions, however, many phenomena such as adsorption, (by)-product formation, and desorption of various species in different phases occur simultaneously, leading to crowded spectra that are difficult to interpret. About 15 years ago, modulation excitation spectroscopy (MES) was introduced to the heterogeneous catalysis community and has been increasingly applied since then. The periodic perturbation of a given system, in combination with phase-sensitive detection (PSD) analysis, significantly reduces noise, distinguishes between active and spectator species, and enables extraction of kinetic information. In this review article, we discuss the origin and theory of MES, summarize different application examples (with an emphasis on heterogeneous catalysis), and suggest future developments of the technique.

Tracking Equilibrium and Nonequilibrium Shifts in Data with TREND

Principal component analysis (PCA) discovers patterns in multivariate data that include spectra, microscopy, and other biophysical measurements. Direct application of PCA to crowded spectra, images, and movies (without selecting peaks or features) was shown recently to identify their equilibrium or temporal changes. To enable the community to utilize these capabilities with a wide range of measurements, we have developed multiplatform software named TREND to Track Equilibrium and Nonequilibrium population shifts among two-dimensional Data frames. TREND can also carry this out by independent component analysis. We highlight a few examples of finding concurrent processes. TREND extracts dual phases of binding to two sites directly from the NMR spectra of the titrations. In a cardiac movie from magnetic resonance imaging, TREND resolves principal components (PCs) representing breathing and the cardiac cycle. TREND can also reconstruct the series of measurements from selected PCs, as illustrated for a biphasic, NMR-detected titration and the cardiac MRI movie. Fidelity of reconstruction of series of NMR spectra or images requires more PCs than needed to plot the largest population shifts. TREND reads spectra from many spectroscopies in the most common formats (JCAMP-DX and NMR) and multiple movie formats. The TREND package thus provides convenient tools to resolve the processes recorded by diverse biophysical methods.

Combined maximum-quantum and DOSY 3D experiments provide enhanced resolution for small molecules in mixtures.

We illustrate here as the combination of high-order maximum-quantum (MaxQ) and Diffusion-Ordered SpectroscopY (DOSY) NMR experiments in a 3D layout allows superior resolution for crowded NMR spectra. Non-uniform sampling (NUS) allows compressing the experimental time effectively to reasonable durations. Because diffusion effects were encoded within multiple-quantum coherences, increased sensitivity to magnetic field gradients is observed, requiring compensation for convection effects. The experiment was demonstrated on the spectra of a mix of small polyaromatic molecules. Specifically, in the case analyzed, the experiment provided an extreme simplification through the MaxQDOSY-MaxQ projection plane that presents one peak per molecule. Copyright © 2016 John Wiley & Sons, Ltd.

High resolution observed in 800MHz DNP spectra of extremely rigid type III secretion needles.

The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800MHz, the resolution of DNP spectra of type III secretion needles (T3SS) could be improved by 22%, indicating that inhomogeneous broadening is not the dominant effect that limits the resolution of T3SS needles under DNP conditions. The outstanding spectral resolution of this system under DNP conditions can be attributed to its low overall flexibility.

Variations of pH as an additional tool in the analysis of crowded NMR spectra of fucosylated chondroitin sulfates

The influence of pH variation on chemical shift values in NMR spectra of fucosylated chondroitin sulfates was studied using polysaccharides isolated from three sea cucumber species Apostichopus japonicus, Actinopyga mauritiana and Cucumaria japonica. The signals of glucuronic acid residues were found to be the most sensitive to pH changes in comparison to the chemical shifts of the sulfated galactosamine and fucosyl units, most of which were altered insignificantly. It was shown that in the presence of imidazole-HCl buffer (pH 7.2) NMR spectra of the polysaccharides from A. japonicus and A. mauritiana were sufficiently resolved, whereas under acidic conditions their 1H NMR spectra were complicated by overlapping of H-1 signals of GlcA and GalNAc. In the case of polysaccharide from C. japonica bearing 3-O-fucosylated and 3-O-sulfated glucuronic acid residues in the backbone, acidification of the medium led to separation of H-1 signals of GlcA3S and GalNAc. Therefore, the combination of data obtained at different pH values may be useful for interpretation of overcrowded spectra of fucosylated chondroitin sulfates.

A Comparative Study of Single-pulse and Double-pulse Laser-Induced Breakdown Spectroscopy with Uranium-containing Samples.

Laser-induced breakdown spectroscopy (LIBS) holds potential advantages in special nuclear material (SNM) sensing and nuclear forensics, which require rapid analysis, minimal sample preparation, and stand-off distance capability. SNM, such as U, however, result in crowded emission spectra with LIBS, and characteristic emission lines are challenging to discern. It is well-known that double-pulse LIBS (DPLIBS) improves the signal intensity for analytes over conventional single-pulse LIBS (SPLIBS). This study investigates the U signal in a glass matrix using DPLIBS and compares it to signal obtained using SPLIBS. Double-pulse LIBS involves sequential firing of a 1.06 µm Nd:YAG pre-pulse and 10.6 µm TEA CO2 heating pulse in a near collinear geometry. Optimization of experimental parameters including inter-pulse delay and energy follows identification of characteristic lines for the bulk analyte Ca and the minor constituent analyte U for both DPLIBS and SPLIBS. Spatial and temporal coupling of the two pulses in the proposed DPLIBS technique yields improvements in analytical merits with a negligible increase in damage to the sample compared to SPLIBS. Subsequently, the study discusses optimum plasma emission conditions of U lines and relative figures of merit in both SPLIBS and DPLIBS. Investigation into plasma characteristics also addresses plausible mechanisms related to the observed U analyte signal variation between SPLIBS and DPLIBS.

A General Method for Extracting Individual Coupling Constants from Crowded 1H NMR Spectra

AbstractCouplings between protons, whether scalar or dipolar, provide a wealth of structural information. Unfortunately, the high number of 1H‐1H couplings gives rise to complex multiplets and severe overlap in crowded spectra, greatly complicating their measurement. Many different methods exist for disentangling couplings, but none approaches optimum resolution. Here, we present a general new 2D J‐resolved method, PSYCHEDELIC, in which all homonuclear couplings are suppressed in F2, and only the couplings to chosen spins appear, as simple doublets, in F1. This approaches the theoretical limit for resolving 1H‐1H couplings, with close to natural linewidths and with only chemical shifts in F2. With the same high sensitivity and spectral purity as the parent PSYCHE pure shift experiment, PSYCHEDELIC offers a robust method for chemists seeking to exploit couplings for structural, conformational, or stereochemical analyses.