Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra.

ENDOR spectroscopy is a fundamental method to detect nuclear spins in the vicinity of paramagnetic centers and their mutual hyperfine interaction. Recently, site-selective introduction of 19F as nuclear labels has been proposed as a tool for ENDOR-based distance determination in biomolecules, complementing pulsed dipolar spectroscopy in the range of angstrom to nanometer. Nevertheless, one main challenge of ENDOR still consists of its spectral analysis, which is aggravated by a large parameter space and broad resonances from hyperfine interactions. Additionally, at high EPR frequencies and fields (⩾94 GHz/3.4 Tesla), chemical shift anisotropy might contribute to broadening and asymmetry in the spectra. Here, we use two nitroxide-fluorine model systems to examine a statistical approach to finding the best parameter fit to experimental 263 GHz 19F ENDOR spectra. We propose Bayesian optimization for a rapid, global parameter search with little prior knowledge, followed by a refinement by more standard gradient-based fitting procedures. Indeed, the latter suffer from finding local rather than global minima of a suitably defined loss function. Using a new and accelerated simulation procedure, results for the semi-rigid nitroxide-fluorine two and three spin systems lead to physically reasonable solutions, if minima of similar loss can be distinguished by DFT predictions. The approach also delivers the stochastic error of the obtained parameter estimates. Future developments and perspectives are discussed.

Cysteine-Based Perfluorinated Derivatives: A Theoretical and Experimental Study.

Cysteine-based perfluoroaromatic (hexafluorobenzene (HFB) and decafluorobiphenyl (DFBP)) were synthesized and established as a chemoselective and available core to construct molecular systems ranging from small molecules to biomolecules with interesting properties. The DFBP was found more effective than HFB for the monoalkylation of decorated thiol molecules. As proof of concept of the potential application of perfluorinated derivatives as non-cleavable linkers, some antibody-perfluorinated conjugates were prepared via thiol through two different strategies, i) using thiol from reduced cystamine coupling to carboxylic acids from mAb by amide bond, and ii) using thiols from reduction of mAb disulfide bond. Conjugates cell binding analysis demonstrated that the bioconjugation does not affect the macromolecular entity. Besides, some molecular properties of synthesized compounds are evaluated through spectroscopic characterization (FTIR and 19 F NMR chemical shifts) and theoretical calculations. The comparison of calculated and experimental 19 F NMR shifts and IR wavenumbers give excellent correlations, asserting as powerful tools in structurally identifying HFB and DFBP derivatives. Moreover, molecular docking was also developed to predict cysteine-based perfluorated derivatives' affinity against topoisomerase Il and cyclooxygenase 2 (COX-2). The results suggested that mainly cysteine-based DFBP derivatives could be potential topoisomerase II α and COX-2 binders, becoming potential anticancer agents and candidates for anti-inflammatory treatment.

Vespa: Integrated applications for RF pulse design, spectral simulation and MRS data analysis.

PURPOSE: The Vespa package (Versatile Simulation, Pulses, and Analysis) is described and demonstrated. It provides workflows for developing and optimizing linear combination modeling (LCM) fitting for 1 H MRS data using intuitive graphical user interface interfaces for RF pulse design, spectral simulation, and MRS data analysis. Command line interfaces for embedding workflows in MR manufacturer platforms and utilities for synthetic dataset creation are included. Complete provenance is maintained for all steps in workflows. THEORY AND METHODS: Vespa is written in Python for compatibility across operating systems. It embeds the PyGAMMA spectral simulation library for spectral simulation. Multiprocessing methods accelerate processing and visualization. Applications use the Vespa database for results storage and cross-application access. Three projects demonstrate pulse, sequence, simulation, and data analysis workflows: (1) short TE semi-LASER single-voxel spectroscopy (SVS) LCM fitting, (2) optimizing MEGA-PRESS (MEscher-GArwood Point RESolved Spectroscopy) flip angle and LCM fitting, and (3) creating a synthetic short TE dataset. RESULTS: The LCM workflows for in vivo basis set creation and spectral analysis showed reasonable results for both the short TE semi-LASER and MEGA-PRESS. Examples of pulses, simulations, and data fitting are shown in Vespa application interfaces for various steps to demonstrate the interactive workflow. CONCLUSION: Vespa provides an efficient and extensible platform for characterizing RF pulses, pulse design, spectral simulation optimization, and automated LCM fitting via an interactive platform. Modular design and command line interface make it easy to embed in other platforms. As open source, it is free to the MRS community for use and extension. Vespa source code and documentation are available through GitHub.

A sub-ppbv-level Acetone and Ethanol Quantum Cascade Laser Based Photoacoustic Sensor - Characterization and Multi-Component Spectra Recording in Synthetic Breath.

Trace gas analysis in breath is challenging due to the vast number of different components. We present a highly sensitive quantum cascade laser based photoacoustic setup for breath analysis. Scanning the range between 8263 and 8270 nm with a spectral resolution of 48 pm, we are able to quantify acetone and ethanol within a typical breath matrix containing water and CO2. We photoacoustically acquired spectra within this region of mid-infra-red light and prove that those spectra do not suffer from non-spectral interferences. The purely additive behavior of a breath sample spectrum was verified by comparing it with the independently acquired single component spectra using Pearson and Spearman correlation coefficients. A previously presented simulation approach is improved and an error attribution study is presented. With a 3σ detection limit of 6.5 ppbv in terms of ethanol and 250 pptv regarding acetone, our system is among the best performing presented so far.

Self-driven super water vapor-absorbing calcium alginate-based bionic leaf for Vis-NIR spectral simulation.

Most bionic leaves cannot autonomously absorb water and maintain high water content like plant leaves, causing the low Vis-NIR spectral similarity to plant leaves. Herein, inspired by the transpiration of plant leaves, a self-driven water vapor-absorbing bionic leaf was prepared by the crosslinking between hygroscopic CaCl2 and sodium alginate (SA) on the visible spectral simulating materials (VSSM). Based on the synergistic effect of the hygroscopicity of CaCl2 and the hydrophilia of calcium alginate (CaAlg), the bionic leaf automatically absorbed water vapor from the air according to ambient humidity and temperature. The water vapor-absorbing property of the bionic leaf was adjusted by changing the CaCl2 concentration (5 wt%-40 wt%), and stable water content of 9.0 %-43.3 % can be obtained in relative humidity of 40-80 %. The CaAlg-based bionic leaf embodied a high spectral correlation coefficient (rm ~ 0.987) for the Vis-NIR spectral simulation of plant leaves. The self-driven water vapor absorbing bionic leaves prepared by CaAlg and CaCl2 provide new insights for the application of bionics, water harvesting from the air, environmental humidity management, and camouflage.

Computational simulation of 1 H NMR profiles of complex biofluid analyte mixtures at differential operating frequencies: Applications to low-field benchtop spectra.

Estimations of accurate and reliable NMR chemical shift values, coupling patterns and constants within a reasonable timeframe remain significantly challenging, and the unavailability of reliable software strategies for the prediction of low-field (e.g., 60 MHz) spectra from those acquired at higher operating frequencies hampers their direct comparison. Hence, this study explored the applications of accessible software options for predicting these parameters in the 1 H NMR profiles of analytes as a function of magnetic field strength; this was performed for individual analytes and also for complex biofluid matrices featured in metabolomics investigations. For this purpose, results from the very first successful experimental acquisition and simulation of the 1 H NMR profiles of intact human salivary supernatant samples on a 60 MHz benchtop spectrometer were evaluated. Using salivary metabolite concentrations determined at 400 MHz, it was demonstrated that simulation of the low-field spectra of five biomolecules with the most prominent 1 H resonances detectable allowed multiple component fits to be applied to experimental spectra. Hence, these salivary 1 H NMR profiles could be successfully predicted throughout the 45-600 MHz operating frequency range. With the exception of propionate resonance multiplets, which revealed more complex coupling patterns at low field and required more astute computational and fitting options, valuable quantitative metabolomics data on salivary acetate, formate, methanol and glycine could be attained from low-field spectrometres. These studies are both timely and pertinent in view of the recent advancement of low-field benchtop NMR facilities for diagnostically significant biomarker tracking in biofluids. Experiments performed with added ammonium chloride to facilitate the release of salivary metabolites from biopolymer binding sites provided evidence that a small but nevertheless significant proportion of propionate, but not lactate, was bound to such sites, an observation of much relevance to biomolecule quantification in salivary metabolomics investigations.

Resolution of chemical shift anisotropy in 19F ENDOR spectroscopy at 263 GHz/9.4 T.

Pulsed 19F ENDOR spectroscopy provides a selective method for measuring angstrom to nanometer distances in structural biology. Here, the performance of 19F ENDOR at fields of 3.4 T and 9.4 T is compared using model compounds containing one to three 19F atoms. CF3 groups are included in two compounds, for which the possible occurrence of uniaxial rotation might affect the distance distribution. At 9.4 T, pronounced asymmetric features are observed in many of the presented 19F ENDOR spectra. Data analysis by spectral simulations shows that these features arise from the chemical shift anisotropy (CSA) of the 19F nuclei. This asymmetry is also observed at 3.4 T, albeit to a much smaller extent, confirming the physical origin of the effect. The CSA parameters are well consistent with DFT predicted values and can be extracted from simulation of the experimental data in favourable cases, thereby providing additional information about the geometrical and electronic structure of the spin system. The feasibility of resolving the CSA at 9.4 T provides important information for the interpretation of line broadening in ENDOR spectra also at lower fields, which is relevant for developing methods to extract distance distributions from 19F ENDOR spectra.

Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation.

The aim of this study was to develop a novel software platform for the simulation of magnetic resonance spin systems, capable of simulating a large number of spatial points (1283 ) for large in vivo spin systems (up to seven coupled spins) in a time frame of the order of a few minutes. The quantum mechanical density-matrix formalism is applied, a coherence pathway filter is utilized for handling unwanted coherence pathways, and the 1D projection method, which provides a substantial reduction in computation time for a large number of spatial points, is extended to include sequences of an arbitrary number of RF pulses. The novel software package, written in MATLAB, computes a basis set of 23 different metabolites (including the two anomers of glucose, seven coupled spins) with 1283 spatial points in 26 min for a three-pulse experiment on a personal desktop computer. The simulated spectra are experimentally verified with data from both phantom and in vivo MEGA-sLASER experiments. Recommendations are provided regarding the various assumptions made when computing a basis set for in vivo MRS with respect to the number of spatial points simulated and the consideration of relaxation.

Retrieval of Hyperspectral Information from Multispectral Data for Perennial Ryegrass Biomass Estimation.

The use of spectral data is seen as a fast and non-destructive method capable of monitoring pasture biomass. Although there is great potential in this technique, both end users and sensor manufacturers are uncertain about the necessary sensor specifications and achievable accuracies in an operational scenario. This study presents a straightforward parametric method able to accurately retrieve the hyperspectral signature of perennial ryegrass (Lolium perenne) canopies from multispectral data collected within a two-year period in Australia and the Netherlands. The retrieved hyperspectral data were employed to generate optimal indices and continuum-removed spectral features available in the scientific literature. For performance comparison, both these simulated features and a set of currently employed vegetation indices, derived from the original band values, were used as inputs in a random forest algorithm and accuracies of both methods were compared. Our results have shown that both sets of features present similar accuracies (root mean square error (RMSE) ≈490 and 620 kg DM/ha) when assessed in cross-validation and spatial cross-validation, respectively. These results suggest that for pasture biomass retrieval solely from top-of-canopy reflectance (ranging from 550 to 790 nm), better performing methods do not rely on the use of hyperspectral or, yet, in a larger number of bands than those already available in current sensors.

Subpixel detection of peanut in wheat flour using a matched subspace detector algorithm and near-infrared hyperspectral imaging.

The detection of adulterations in food powder products represents a high interest especially when it concerns the health of the consumers. The food industry is concerned by peanut adulteration since it is a major food allergen often used in transformed food products. Near-infrared hyperspectral imaging is an emerging technology for food inspection. It was used in this work to detect peanut flour adulteration in wheat flour. The detection of peanut particles was challenging for two reasons: the particle size is smaller than the pixel size leading to impure spectral profiles; peanut and wheat flour exhibit similar spectral signatures and variability. A Matched Subspace Detector (MSD) algorithm was designed to take these difficulties into account and detect peanut adulteration at the pixel scale using the associated spectrum. A set of simulated data was generated to overcome the lack of reference values at the pixel scale and to design appropriate MSD algorithms. The best designs were compared by estimating the detection sensitivity. Defatted peanut flour and wheat flour were mixed in eight different proportions (from 0.02% to 20%) to test the detection performances of the algorithm on real hyperspectral measurements. The number and positions of the detected pixels were investigated to show the relevancy of the results and validate the design of the MSD algorithm. The presented work proved that the use of hyperspectral imaging and a fine-tuned MSD algorithm enables to detect a global adulteration of 0.2% of peanut in wheat flour.

Rotamers of p­isopropylphenol studied by hole-burning resonantly enhanced multiphoton ionization and mass analyzed threshold ionization spectroscopy.

The resonance enhanced multiphoton ionization (REMPI), ultraviolet-ultraviolet (UV-UV) hole burning and mass analyzed threshold ionization (MATI) spectroscopy have been applied to investigate the vibrational features of p­isopropylphenol in its first electronically excited state S1 and cationic ground state D0. Two stable conformational structures of p­isopropylphenol are distinctly found in the supersonic molecular beam and identified as the cis and trans rotamers through REMPI and UV-UV hole burning spectroscopy. The electronic excitation energies of S1 ← S0 transition of two rotamers are determined to be 35,578 and 35,593 cm-1, and the adiabatic ionization energies are 65,331 and 65,350 cm-1, respectively. The MATI spectra recorded via different intermediate levels of S1 state indicate the similarity in the molecular geometry between the S1 state and the D0 state for each rotamer of p­isopropylphenol. Geometrical optimizations of p­isopropylphenol have also been performed using the density functional theory (DFT) for S0 and D0 states, and time-dependent density functional theory (TDDFT) for S1 state. The simulated spectra for S1 ← S0 and D0 ← S1 transitions of two rotamers are able to reproduce qualitatively the experimental spectral profile, which help us to assign the vibronic modes. Most of the observed vibrations of two rotamers in the S1 and D0 states are related to the in-plane ring deformation and some active modes involving isopropyl group.

Advanced processing and simulation of MRS data using the FID appliance (FID-A)-An open source, MATLAB-based toolkit.

PURPOSE: To introduce a new toolkit for simulation and processing of magnetic resonance spectroscopy (MRS) data, and to demonstrate some of its novel features. METHODS: The FID appliance (FID-A) is an open-source, MATLAB-based software toolkit for simulation and processing of MRS data. The software is designed specifically for processing data with multiple dimensions (eg, multiple radiofrequency channels, averages, spectral editing dimensions). It is equipped with functions for importing data in the formats of most major MRI vendors (eg, Siemens, Philips, GE, Agilent) and for exporting data into the formats of several common processing software packages (eg, LCModel, jMRUI, Tarquin). This paper introduces the FID-A software toolkit and uses examples to demonstrate its novel features, namely 1) the use of a spectral registration algorithm to carry out useful processing routines automatically, 2) automatic detection and removal of motion-corrupted scans, and 3) the ability to perform several major aspects of the MRS computational workflow from a single piece of software. This latter feature is illustrated through both high-level processing of in vivo GABA-edited MEGA-PRESS MRS data, as well as detailed quantum mechanical simulations to generate an accurate LCModel basis set for analysis of the same data. RESULTS: All of the described processing steps resulted in a marked improvement in spectral quality compared with unprocessed data. Fitting of MEGA-PRESS data using a customized basis set resulted in improved fitting accuracy compared with a generic MEGA-PRESS basis set. CONCLUSIONS: The FID-A software toolkit enables high-level processing of MRS data and accurate simulation of in vivo MRS experiments. Magn Reson Med 77:23-33, 2017. © 2015 Wiley Periodicals, Inc.

Confident site localization using a simulated phosphopeptide spectral library.

We have investigated if phosphopeptide identification and simultaneous site localization can be achieved by spectral library searching. This allows taking advantage of comparison of specific spectral features, which would lead to improved discrimination of differential localizations. For building a library, we propose a spectral simulation strategy where all possible single phosphorylations can be simply and accurately (re)constructed on enzymatically dephosphorylated peptides, by predicting the diagnostic fragmentation events produced in beam-type CID. To demonstrate the performance of our approach, enriched HeLa phosphopeptides were dephosphorylated with alkaline phosphatase and analyzed with higher energy collisional dissociation (HCD), which were then used for creating a spectral library of simulated phosphopeptides. Spectral library searching using SpectraST was performed on data sets of synthetic phosphopeptides and the HeLa phosphopeptides, and subsequently compared to Mascot and Sequest database searching followed by phosphoRS and Ascore afforded localization, respectively. Our approach successfully led to accurate localization, and it outperformed other methods, when phosphopeptides were covered by the library. These results suggest that the searching with simulated spectral libraries serves as a crucial approach for both supplementing and validating the phosphorylation sites obtained by database searching and localization tools. For future development, simulation of multiply phosphorylated peptides remains to be implemented.

DFT 1H-1H coupling constants in the conformational analysis and stereoisomeric differentiation of 6-heptenyl-2H-pyran-2-ones: configurational reassignment of synargentolide A.

Density functional theory (DFT) (1) H-(1) H NMR coupling constant calculations, including solvation parameters with the polarizable continuum model B3LYP/DGDZVP basis set together with the experimental values measured by spectral simulation, were used to predict the configuration of hydroxylated 6-heptenyl-5,6-dihydro-2H-pyran-2-ones 1, 2, 4, and 7, allowing epimer differentiation. Modeling of these flexible compounds requires the inclusion of solvation models that account for stabilizing interactions derived from intramolecular and intermolecular hydrogen bonds, in contrast with peracetylated derivatives (3, 5, and 6) in which the solvation consideration can be omitted. Using this DFT NMR integrated approach as well as spectral simulation, the configurational reassignment of synargentolide A (8) was accomplished by calculations in the gas phase among four possible diastereoisomers (8-11). Calculated (3) JH,H values established its configuration as 6R-[4'S,5'S,6'S-(triacetyloxy)-2E-heptenyl]-5,6-dihydro-2H-pyran-2-one (8), in contrast with the incorrect 6R,4'R,5'R,6'R-diastereoisomer previously proposed by synthesis (12). Application of this approach increases the probability for successful enantiospecific total syntheses of flexible compounds with multiple chiral centers.

Optimization of bicelle lipid composition and temperature for EPR spectroscopy of aligned membranes.

We have optimized the magnetic alignment of phospholipid bilayered micelles (bicelles) for EPR spectroscopy, by varying lipid composition and temperature. Bicelles have been extensively used in NMR spectroscopy for several decades, in order to obtain aligned samples in a near-native membrane environment and take advantage of the intrinsic sensitivity of magnetic resonance to molecular orientation. Recently, bicelles have also seen increasing use in EPR, which offers superior sensitivity and orientational resolution. However, the low magnetic field strength (less than 1 T) of most conventional EPR spectrometers results in homogeneously oriented bicelles only at a temperature well above physiological. To optimize bicelle composition for magnetic alignment at reduced temperature, we prepared bicelles containing varying ratios of saturated (DMPC) and unsaturated (POPC) phospholipids, using EPR spectra of a spin-labeled fatty acid to assess alignment as a function of lipid composition and temperature. Spectral analysis showed that bicelles containing an equimolar mixture of DMPC and POPC homogeneously align at 298 K, 20 K lower than conventional DMPC-only bicelles. It is now possible to perform EPR studies of membrane protein structure and dynamics in well-aligned bicelles at physiological temperatures and below.

Enamel dose calculation by electron paramagnetic resonance spectral simulation technique / 中华放射医学与防护杂志

Objective To optimize the enamel electron paramagnetic resonance (EPR) spectral processing by using the EPR spectral simulation method to improve the accuracy of enamel EPR dosimetry and reduce artificial error.Methods The multi-component superimposed EPR powder spectral simulation software was developed to simulate EPR spectrum models of the background signal(BS) and the radiation- induced signal (RS) of irradiated enamel respectively.RS was extracted from the multi-component superimposed spectrum of irradiated enamel and its amplitude was calculated.The dose-response curve was then established for calculating the doses of a group of enamel samples.The result of estimated dose was compared with that calculated by traditional method.Results BS was simulated as a powder spectrum of gaussian line shape with the following spectrum parameters:g =2.00 35 and Hpp =0.65 - 1.1 mT,RS signal was also simulated as a powder spectrum but with axi-symmetric spectrum characteristics.The spectrum parameters of RS were:g(1) =2.0018,g (11) =1.996 5,Hpp =0.335 - 0.4 mT.The amplitude of RS had a linear response to radiation dose with the regression equation as y =240.74x + 76 724 ( R2 =0.9947 ).The expectation of relative error of dose estimation was 0.13.Conclusions EPR simulation method has improved somehow the accuracy and reliability of enamel EPR dose estimation.