Spectral Calculations Research Articles

Statistical data analysis of x-ray spectroscopy data enabled by neural network accelerated Bayesian inference.

Bayesian inference applied to x-ray spectroscopy data analysis enables uncertainty quantification necessary to rigorously test theoretical models. However, when comparing to data, detailed atomic physics and radiation transfer calculations of x-ray emission from non-uniform plasma conditions are typically too slow to be performed in line with statistical sampling methods, such as Markov Chain Monte Carlo sampling. Furthermore, differences in transition energies and x-ray opacities often make direct comparisons between simulated and measured spectra unreliable. We present a spectral decomposition method that allows for corrections to line positions and bound-bound opacities to best fit experimental data, with the goal of providing quantitative feedback to improve the underlying theoretical models and guide future experiments. In this work, we use a neural network (NN) surrogate model to replace spectral calculations of isobaric hot-spots created in Kr-doped implosions at the National Ignition Facility. The NN was trained on calculations of x-ray spectra using an isobaric hot-spot model post-processed with Cretin, a multi-species atomic kinetics and radiation code. The speedup provided by the NN model to generate x-ray emission spectra enables statistical analysis of parameterized models with sufficient detail to accurately represent the physical system and extract the plasma parameters of interest.

2, 9-deoxyflavonoids (= 3-aryl-1-indanones) from Aglaia odorata: Structure elucidation, biosynthetic pathway and lung protective activity

Six previously undescribed 2, 9-deoxyflavonoids (1/2a, 1/2b, 6, and 7), along with six known compounds (3–5, and 8–10), were isolated from the twigs and leaves of Aglaia odorata. Their structures were determined by a combination of spectral analysis, ECD calculation and enzymatic hydrolysis assay. Surprisingly, (±) aglaindanone E (11a, 11b) were unexpectedly formed as the derivatives of compounds 3–6 when exposed to ambient natural light. Furthermore, the plausible biosynthetic pathway of 2, 9-deoxyflavonoids was proposed and chemically mimicked. In biological activity assay, compounds 1/2a, 1/2b, 4, and 6 showed potential protective effects in the 0.75%CSE-induced BEAS-2B cells injury model.

Unusual cadinane-involved sesquiterpenoid dimers from Artemisia annua and their antihepatoma effect

Artemisia annua L. (“Qinghao” in Chinese) is a famous traditional Chinese medicinal herb and has been used to treat malaria and various tumors. Our preliminary screening indicated that the EtOAc extract of A. annua manifested activity against HepG2, Huh7, and SK-Hep-1 cell lines with inhibitory ratios of 53.2%, 52.1%, and 59.6% at 200 μg/mL, respectively. Bioassay-guided isolation of A. annua afforded 14 unusual cadinane-involved sesquiterpenoid dimers, artemannuins A‒N (1–14), of which the structures were elucidated by extensive spectral analyses, ECD calculations, and single-crystal X-ray diffraction. Structurally, these compounds were classified into five different types based on the coupled modes of two monomeric sesquiterpenoids. Among them, compounds 1–9 represented the first examples of sesquiterpenoid dimers formed via the C-3‒C-3′ single bond of two 5(4 → 3)-abeo-cadinane sesquiterpenoid monomers, while compounds 13 and 14 were dimers fused by cadinane and humulane sesquiterpenoids via an ester bond. Methylated derivatives of 1, 4, 6, and 8 showed antihepatoma activity against HepG2, Huh7, and SK-Hep-1 cell lines with IC50 values ranging from 30.5 to 57.2 μM.

Second-order spectral line shift comparisons

The second-order spectral line width formulae from the projection operator and kinetic theory methods were recently compared. It was shown that a systematic expansion of the projection operator width expression including initial correlations formally agrees with the second-order kinetic theory result. It is now shown that the second-order dynamic shifts are also formally the same. The static shifts, however, differ due to an ad hoc treatment of electron-electron correlations in the projection operator method. The approximation is necessary in order to screen the radiator-electron interactions. The differences, however, are expected to be small. The results suggest using the rigorous and more compact second-order width and shift expressions from the kinetic theory method as the starting point for spectral line shape calculations. At line center, however, the projection operator second-order expression for the width and shift simplifies and reduces to the kinetic theory result.

Novel Dual-Emission Emitters Featuring Phenothiazine-S-Oxide and Phenothiazine-S,S-Dioxide Motifs.

In this study, we have successfully designed and synthesized two novel dual-emission emitters featuring phenothiazine-5-oxide and phenothiazine-5,5-dioxide motifs, characterized by highly lopsided and asymmetric conformational states. Through rigorous spectral examinations and DFT calculations, the compounds exhibit distinctive ICT phenomena, coupled with efficient emission in solid states and AIEE characteristics under high water fractions in DMF/H2O mixtures. These non-planar luminogens exhibit vibrant green and blue solid-state luminescence, with fluorescence quantum yields of 24.1 % and 15.21 %, respectively. Additionally, they both emit green fluorescence in THF solution, with notable emission quantum yields (QYs) 36.4 % and 30.4 %. Comprehensive theoretical investigations unveil well-defined electron cloud density separation between the energies of HOMO/LUMO levels within the two luminogens. Notably, the targeted molecule harboring the phenothiazine-S,S-dioxide motif also demonstrates remarkable reversible mechanofluorochromic properties. Moreover, we testify their potential in applications such as solid-state rewritable information storage and live-cell imaging in solution states. Through theoretical calculations and comparative studies, we have explored the intrinsic relationship between molecular structure and performance, effectively screening and identifying new fluorescent molecules exhibiting outstanding luminescent attributes. These discoveries establish a robust theoretical and technical foundation for the synthesis and application of efficient DSE-based MFC materials, opening new avenues in the realm of advanced luminescent materials.

New cembranoid with potent anti-inflammatory effect isolated from Boswellia sacra by inactivating the NF-κB signaling pathway

Boswellia sacra has the properties of activating blood circulation, fixing pain, subduing swelling and promoting muscle growth. However, the anti-inflammatory active ingredients and molecular mechanisms of Boswellia sacra are still not clearly explored. Boswellia sacra was grounded and extracted using 95% ethanol, the extracts were separated by column chromatography preparation to give compounds. Spectral analysis and quantum calculations confirmed the structures of compounds and identified compound 1 as a new compound. Compounds 1–3 showed potent inhibitory activities and their effects on inflammatory mediator NO and inflammatory cytokines were examined by ELISA assay. Furthermore, their modulatory mechanism on inflammatory signal pathways was explored.

Fast and accurate prediction of interference spectra of non-adiabatic tapered microfiber Mach-Zehnder interferometer in liquid

Microfiber Mach-Zehnder interferometer (MMZI) is a widely used optical device. To solve the problems of large difference between the theoretical and experimental spectrum, low calculation efficiency, poor universality in spectrum calculation of MMZI, a fast and accurate calculation method for predicting the interference spectrum of MMZI used in liquid is proposed. In calculations, phase accumulated in transition region of the taper is considered to reach a good agreement between theoretical and experimental spectrum. To further improve the computational efficiency, dependence of the phase accumulation on wavelength is developed by linear fitting, and a non-linear fitting of difference of effective refractive index (∆neff) on fiber diameter, wavelength, temperature and salinity of the surrounding is obtained by the data from commercial software. In addition, a visual interface for displaying the predicted spectrum is established, by which one accurate spectral calculation can be realized within only two or three seconds. Finally, effects of LP03 mode and shape of transition region on transmission spectrum are discussed and the accuracy of this method is also verified by sensitivity. The calculation method demonstrated here provides an accurate and fast spectral prediction method for MMZI, and will afford important reference for sensor design and optimization.

Solid-state vibrational circular dichroism for pharmaceutical applications: Polymorphs and cocrystal of sofosbuvir

X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree of expertise. Vibrational circular dichroism (VCD) spectroscopy resolves these limitations, while also exhibiting substantial sensitivity to subtle modifications in the conformation and molecular packaging in the solid state. This study showcases VCD’s ability to differentiate between various crystal structures of the same molecule (polymorphs, cocrystals). We examined the most effective approach for producing high-quality spectra and unveiled the intricate link between structure and spectrum via quantum-chemical computations. We rigorously assessed, using alanine as a model compound, multiple experimental conditions on the resulting VCD spectra, with the aim of proposing an optimal and efficient procedure. The proposed approach, which yields reliable, reproducible, and artifact-free results with maximal signal-to-noise ratio, was then validated using a set comprising of three amino acids (serine, alanine, tyrosine), one hydroxy acid (tartaric acid), and a monosaccharide (ribose) to mimic active pharmaceutical components. Finally, the optimized approach was applied to distinguish three polymorphs of the antiviral drug sofosbuvir and its cocrystal with piperazine. Our results indicate that solid-state VCD is a prompt, cost-effective, and easy-to-use technique to identify crystal structures, demonstrating potential for application in pharmaceuticals. We also adapted the cluster and transfer approach to calculate the spectral properties of molecules in a periodic crystal environment. Our findings demonstrate that this approach reliably produces solid-state VCD spectra of model compounds. Although for large molecules with many atoms per unit cell, such as sofosbuvir, this approach has to be simplified and provides only a qualitative match, spectral calculations, and energy analysis helped us to decipher the observed differences in the experimental spectra of sofosbuvir.

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling.

Fully atomistic multiscale polarizable quantum mechanics (QM)/molecular mechanics (MM) approaches, combined with techniques to sample the solute-solvent phase space, constitute the most accurate method to compute spectral signals in aqueous solution. Conventional sampling strategies, such as classical molecular dynamics (MD), may encounter drawbacks when the conformational space is particularly complex, and transition barriers between conformers are high. This can lead to inaccurate sampling, which can potentially impact the accuracy of spectral calculations. For this reason, in this work, we compare classical MD with enhanced sampling techniques, i.e., replica exchange MD and metadynamics. In particular, we show how the different sampling techniques affect computed UV, electronic circular dichroism, nuclear magnetic resonance shielding, and optical rotatory dispersion of N-acetylproline-amide in aqueous solution. Such a system is a model peptide characterized by complex conformational variability. Calculated values suggest that spectral properties are influenced by solute conformers, relative population, and solvent effects; therefore, particular care needs to be paid for when choosing the sampling technique.

In situ fabrication of 2D Bi/Bi2O2CO3 nanosheets anchored on Bi substrate for highly-efficient photoelectrocatalytic CO2 reduction to formate

Utilizing photoelectrocatalysis for the CO2 conversion into value-added chemicals presents a promising approach for alleviating energy-environmental crisis, but the current catalysts encounter the limitations of electron transfer efficiency, activity and stability. Herein, we in situ construct Bi/Bi2O2CO3 composite film with nanosheets anchored on Bi substrate to optimize reaction kinetics, and effectively enhance the separation and transport efficiencies of photogenerated carriers. Our findings reveal that the formate Faraday efficiency of 92.68 % at −0.95 V (vs. RHE) for photoelectrocatalytic CO2 reduction over Bi/Bi2O2CO3 film is much higher obviously than 84 % of electrocatalytic CO2 reduction reaches, and there is no significant decrease within 10 h of activity test. Besides, the highest applied bias photon-to-current efficiency and cathode energy efficiency can achieve 1.19 % and 61 %, respectively, indicating the superior energy utilization of the catalyst. Finally, a reasonable electron transfer mechanism for the enhanced photoelectrocatalytic CO2 reduction over Bi/Bi2O2CO3 film is proposed and clarified based on the spectral characterizations and density functional theory calculations. This work should provide a novel perspective for the design and research of Bi-based photocathodes.

Spectral gaps of two- and three-dimensional many-body quantum systems in the thermodynamic limit

We present an expression for the spectral gap, opening up new possibilities for performing and accelerating spectral calculations of quantum many-body systems. We develop and demonstrate one such possibility in the context of tensor network simulations. Our approach requires only minor modifications of the widely used simple update method and is computationally lightweight relative to other approaches. We validate it by computing spectral gaps of the 2D and 3D transverse-field Ising models and find strong agreement with previously reported perturbation theory results. Published by the American Physical Society 2024

Phase Transition and Luminescent Property Change Induced by Different Organic Cations in One-Dimensional Double Perovskites.

Double perovskites (DPs) have attracted attention in the field of luminescence due to their inherent broadband emission of self-trapping excitons. In this work, we choose [(CH3)3NCH2CHCH2]+ and [CH3CHOHCH2NH2]+ as organic cations to synthesize two new organic-inorganic hybrid DPs, [(CH3)3NCH2CHCH2]2KInCl6 (1) and [CH3CHOHCH2NH2]2KInCl6 (2). The [KCl6]3- and [InCl6]3- octahedra are interchangeably connected by sharing two opposite faces, forming a one-dimensional coordination chain. Each K atom coordinates with six chlorine atoms in 1, while it coordinates with two oxygen atoms in addition to the six chlorine atoms in 2. The coordination between ions K and O in compound 2 may have significantly reduced its luminescence. As a result, compound 1 shows bright-yellow light with a quantum yield of more than 90%, while 2 shows weak blue light with a quantum yield of only 0.98%. In addition, different from no phase transition found in 2, 1 undergoes a reversible phase transition at 324/307 K in the heating-cooling cycle. Through structural and spectral analysis and density functional theory calculation, we conclude that the larger degree of [InCl6]3- octahedral distortion and the larger anion distance (In···In) also cause the PLQY of compound 1 to be higher than that of compound 2.

Estimation of Maize Residue Cover Using Remote Sensing Based on Adaptive Threshold Segmentation and CatBoost Algorithm

Maize residue cover (MRC) is an important parameter to quantify the degree of crop residue cover in the field and its spatial distribution characteristics. It is also a key indicator of conservation tillage. Rapid and accurate estimation of maize residue cover (MRC) and spatial mapping are of great significance to increasing soil organic carbon, reducing wind and water erosion, and maintaining soil and water. Currently, the estimation of maize residue cover in large areas suffers from low modeling accuracy and poor working efficiency. Therefore, how to improve the accuracy and efficiency of maize residue cover estimation has become a research hotspot. In this study, adaptive threshold segmentation (Yen) and the CatBoost algorithm are integrated and fused to construct a residue coverage estimation method based on multispectral remote sensing images. The maize planting areas in and around Sihe Town in Jilin Province, China, were selected as typical experimental regions, and the unmanned aerial vehicle (UAV) was employed to capture maize residue cover images of sample plots within the area. The Yen algorithm was applied to calculate and analyze maize residue cover. The successive projections algorithm (SPA) was used to extract spectral feature indices from Sentinel-2A multispectral images. Subsequently, the CatBoost algorithm was used to construct a maize residue cover estimation model based on spectral feature indices, thereby plotting the spatial distribution map of maize residue cover in the experimental area. The results show that the image segmentation based on the Yen algorithm outperforms traditional segmentation methods, with the highest Dice coefficient reaching 81.71%, effectively improving the accuracy of maize residue cover recognition in sample plots. By combining the spectral index calculation with the SPA algorithm, the spectral features of the images are effectively extracted, and the spectral feature indices such as NDTI and STI are determined. These indices are significantly correlated with maize residue cover. The accuracy of the maize residue cover estimation model built using the CatBoost model surpasses that of traditional machine learning models, with a maximum determination coefficient (R2) of 0.83 in the validation set. The maize residue cover estimation model constructed based on the Yen and CatBoost algorithms effectively enhances the accuracy and reliability of estimating maize residue cover in large areas using multispectral imagery, providing accurate and reliable data support and services for precision agriculture and conservation tillage.

Assessment of Site Effects and Numerical Modeling of Seismic Ground Motion to Support Seismic Microzonation of Dushanbe City, Tajikistan

In the territory of Dushanbe city, the capital of Tajikistan, detailed geological and geophysical data were collected during geophysical surveys in 2019–2020. The data comprise 5 microtremor array measurements, 9 seismic refraction tomography profiles, seismological data from 5 temporary seismic stations for standard spectral ratio calculations, 60 borehole datasets, and 175 ambient noise measurements. The complete dataset for Dushanbe was used to build a consistent 3D geologic model of the city with a size of 12 × 12 km2. The results of the seismological and geophysical surveys were compared and calibrated with borehole data to define the boundaries of each layer in the study area. The Leapfrog Works software was utilized to create a 3D geomodel. From the 3D geomodel, we extracted six 12 km long 2D geological cross-sections. These 2D geological cross-sections were used for 2D dynamic numerical modeling with the Universal Distinct Element Code software to calculate the local seismic response. Finally, the dynamic numerical modeling results were compared with the amplification functions obtained from the seismological and ambient noise data analysis. The 2D dynamic numerical modeling results allowed a better assessment of the site effects in the study area to support seismic microzonation and the determination of local peak ground acceleration changes in combination with regional seismic hazard maps. In addition, our results confirm the strong seismic amplification effects noted in some previous studies, which are attributed to the influence of local topographic and subsurface characteristics on seismic ground motions.

Enhanced performance of attapulgite-supported g-C3N4 for photocatalytic CO2 reduction

As a new type of non-metallic semiconductor photocatalyst, g-C3N4 has great potential in photocatalytic CO2 reduction. However, due to the low catalytic activity, it is still far from industrial reality for such applications. Herein, this work introduces attapulgite (ATP) into the photocatalyst system of g-C3N4. Additionally, ATP/Au-CN was obtained through the photodeposition method. The photocatalytic reduction ability of the photocatalyst for CO2 is enhanced. The photoelectric tests show that loading of ATP can promote the separation and migration of photocarriers. Through BET testing, it was found that the alkaline pore structure on the surface of ATP not only captures CO2, but also increases the specific surface area of the composite. According to the experimental results, the possible photocatalytic mechanism was verified by in-situ diffuse reflection infrared Fourier transform (DRIFT) spectral analysis and DFT calculation. This work provides new guidance for the construction of high efficient photocatalyst systems using abundant ATP as a support.

Artemyriantholides A–K, guaiane-type sesquiterpenoid dimers from Artemisia myriantha var. pleiocephala and their antihepatoma activity

Artemyriantholides A−K (1−11) as well as 14 known compounds (12−25) were isolated from Artemisia myriantha var. pleiocephala (Asteraceae). The structures and absolute configuration of compounds 2 and 8−9 were confirmed by the single crystal X-ray diffraction analyses, and the others were elucidated by MS, NMR spectral data and electronic circular dichroism calculations. All compounds were chemically characterized as guaiane-type sesquiterpenoid dimers (GSDs). Compound 1 was the first example of the GSD fused via C-3/C-11′ and C-5/C-13′ linkages, and compounds 2 and 5 were rare GSDs containing chlorine atoms. Eleven compounds showed obvious inhibitory activity in HepG2, Huh7 and SK-Hep-1 cell lines by antihepatoma assay to provide the IC50 values ranging from 7.9 to 67.1 μM. Importantly, compounds 5 and 8 exhibited the best inhibitory activity with IC50 values of 14.2 and 18.8 (HepG2), 9.0 and 11.5 (Huh7), and 8.8 and 11.3 μM (SK-Hep-1), respectively. The target of compound 5 was predicted to be MAP2K2 by a computational prediction model. The interaction between compound 5 and MAP2K2 was conducted to give docking score of −9.0 kcal/mol by molecular docking and provide KD value of 43.7 μM by Surface Plasmon Resonance assay.

Computational design and experimental investigation of novel thiophene-based organic dyes with N,N-dimethylaminophenyl and morpholinophenyl donors for dye-sensitized solar cells

A new series of thiophene-based organic chromophores (4–7 a, b) has been developed through structural engineering of the electron donor (D) group, incorporating N,N-dimethylaminophenyl and morpholinophenyl, and acceptor moieties such as benzonitrile and flurobenzonitrile. Additionally, a π-linkage of phenylthiophene was inserted. The effects of various donating and accepting groups, as well as the spacer, on the geometrical, energetic, absorption, and photovoltaic properties of these sensitizers were investigated using Density Functional Theory (DFT) and Time-Dependent DFT. The sensitizers were optimized in their ground state using selected functional methods. Furthermore, key properties such as absorbance, frequency, energies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO), energy gap, dipole moment, and global reactivity descriptors were calculated using quantum chemical calculations. These spectral properties and quantum chemical calculations provide valuable insights into the potential use of these sensitizers in photonic devices. The results obtained from analyzing light harvesting efficiency (LHE), free energy injection (ΔGinj), and open circuit voltage (Voc) demonstrate that these dyes show promising characteristics for future experimental studies and offer guidelines for improving the performance of dye-sensitized solar cells. By employing structural modifications and investigating the electronic properties of these newly developed chromophores, this study contributes to the understanding of their behavior and potential applications in photonic devices. The findings provide a foundation for further experimental investigations and offer valuable insights for the development of more efficient dye-sensitized solar cells.

Radiation transfer in the spectra of short-pulse laser-heated targets

The conditions in laser-produced plasmas are frequently determined with x-ray spectroscopy by comparing calculated to measured spectra. Line spectra from K-shell transitions of low- to mid-atomic number elements are most often used since the important physical processes are well understood and reliable spectra can be readily measured and calculated. Radiation transfer effects due to large optical depths of strong lines can influence the spectra. In this work, the effects of radiation transfer on the emission spectra of short-laser pulse-heated targets are studied. The possible errors made in inferring electron temperature by not including radiation transfer are quantified. The inclusion of radiative transfer in spectral calculations improves the accuracy of typical temperature diagnostics and allows the use of strong lines for diagnostics.

Catalytic Mechanism of Fatty Acid Photodecarboxylase: On the Detection and Stability of the Initial Carbonyloxy Radical Intermediate.

In fatty acid photodecarboxylase (FAP), light-induced formation of the primary radical product RCOO⋅ from fatty acid RCOO- occurs in 300 ps, upon which CO2 is released quasi-immediately. Based on the hypothesis that aliphatic RCOO⋅ (spectroscopically uncharacterized because unstable) absorbs in the red similarly to aromatic carbonyloxy radicals such as 2,6-dichlorobenzoyloxy radical (DCB⋅), much longer-lived linear RCOO⋅ has been suggested recently. We performed quantum chemical reaction pathway and spectral calculations. These calculations are in line with the experimental DCB⋅ decarboxylation dynamics and spectral properties and show that in contrast to DCB⋅, aliphatic RCOO⋅ radicals a) decarboxylate with a very low energetic barrier and on the timescale of a few ps and b) exhibit little red absorption. A time-resolved infrared spectroscopy experiment confirms very rapid, ≪300 ps RCOO⋅ decarboxylation in FAP. We argue that this property is required for the observed high quantum yield of hydrocarbons formation by FAP.

Catalytic Mechanism of Fatty Acid Photodecarboxylase: On the Detection and Stability of the Initial Carbonyloxy Radical Intermediate

AbstractIn fatty acid photodecarboxylase (FAP), light‐induced formation of the primary radical product RCOO⋅ from fatty acid RCOO− occurs in 300 ps, upon which CO2 is released quasi‐immediately. Based on the hypothesis that aliphatic RCOO⋅ (spectroscopically uncharacterized because unstable) absorbs in the red similarly to aromatic carbonyloxy radicals such as 2,6‐dichlorobenzoyloxy radical (DCB⋅), much longer‐lived linear RCOO⋅ has been suggested recently. We performed quantum chemical reaction pathway and spectral calculations. These calculations are in line with the experimental DCB⋅ decarboxylation dynamics and spectral properties and show that in contrast to DCB⋅, aliphatic RCOO⋅ radicals a) decarboxylate with a very low energetic barrier and on the timescale of a few ps and b) exhibit little red absorption. A time‐resolved infrared spectroscopy experiment confirms very rapid, ≪300 ps RCOO⋅ decarboxylation in FAP. We argue that this property is required for the observed high quantum yield of hydrocarbons formation by FAP.