Basis Of Spectroscopic Data Research Articles

Diverse indole-diterpenoids with protein tyrosine phosphatase 1B inhibitory activities from the marine coral-derived fungus Aspergillus sp. ZF-104

Eight previously undescribed indole-diterpenoids named penerpenes O–V (1–8), together with seven known analogues (9–14), were isolated from the marine soft coral-derived fungus Aspergillus sp. ZF-104. Their structures including the absolute configurations of these compounds were assigned on the basis of spectroscopic data and ECD analysis along with quantum ECD and NMR calculations. Compounds 4 and 5 bear rare indolin-2-one units in their structures and 6 bears a reconstructed novel skeleton in which the indole ring and the terpenoid substructure are cleaved before they are reconnected through the nitrogen atom. Compounds 1, 2, 7, and 10 showed protein tyrosine phosphatase 1B (PTP1B) inhibitory activities comparable to that of the positive control NaVO3.

Ab initio quantum scattering calculations and a new potential energy surface for the HCl(X1Σ+)-O2(X3Σg-) system: Collision-induced line shape parameters for O2-perturbed R(0) 0-0 line in H35Cl.

The remote sensing of abundance and properties of HCl-the main atmospheric reservoir of Cl atoms that directly participate in ozone depletion-is important for monitoring the partitioning of chlorine between "ozone-depleting" and "reservoir" species. Such remote studies require knowledge of the shapes of molecular resonances of HCl, which are perturbed by collisions with the molecules of the surrounding air. In this work, we report the first fully quantum calculations of collisional perturbations of the shape of a pure rotational line in H35Cl perturbed by an air-relevant molecule [as the first model system we choose the R(0) line in HCl perturbed by O2]. The calculations are performed on our new highly accurate HCl(X1Σ+)-O2(X3Σg-) potential energy surface. In addition to pressure broadening and shift, we also determine their speed dependencies and the complex Dicke parameter. This gives important input to the community discussion on the physical meaning of the complex Dicke parameter and its relevance for atmospheric spectra (previously, the complex Dicke parameter for such systems was mainly determined from phenomenological fits to experimental spectra and the physical meaning of its value in that context is questionable). We also calculate the temperature dependence of the line shape parameters and obtain agreement with the available experimental data. We estimate the total combined uncertainties of our calculations at 2% relative root-mean-square error in the simulated line shape at 296K. This result constitutes an important step toward computational population of spectroscopic databases with accurate abinitio line shape parameters for molecular systems of terrestrial atmospheric importance.

Ozone spectroscopy in the terahertz range from first high-resolution Synchrotron SOLEIL experiments combined with far-infrared measurements and ab initio intensity calculations

Ozone is one of the important molecules in terms of the impact on the atmospheric chemistry, climate changes, bio- and eco-systems and human health. It has a strong absorption in the microwave, terahertz and far-infrared spectral ranges where a large part of the Earth’s outgoing longwave radiation to space is located. In this work, the observations, and analyses of the ozone high-resolution spectra in the THz range recorded using the Synchrotron light source of the SOLEIL CNRS equipment are reported for the first time. Thanks to the exceptional brightness of the Synchrotron radiation and to the signal/noise ratio, it was possible to observe many more ozone transitions of the cold rotational band and the hot ν2-ν2 band in the range 0.9–6 THz compared to the previous works. In addition, we have carried out new measurements and assignments for the ν2 band. The simultaneous fit of the rotational band GS-GS, the hot band ν2-ν2 and the FIR ν2 band yielded an overall weighted standard deviation of 0.68 for 13,466 line positions within the experimental accuracy. This includes all previously available MW (with the best uncertainty 0.1 – 10 kHz), FIR data and the original SOLEIL measurements that provided experimental accuracy of 0.00005 – 0.0001 cm−1 for the best lines. Significant deviations in new experimental spectra compared to available spectroscopic databases were evidenced, particularly for the line positions and energy levels at high J, Ka rotational quantum numbers that are the most pronounced in the 4.5 – 6 THz range. Accurate ab initio calculations of line intensities combined with empirically fitted line positions were used to create new linelists that permit theoretical modelling of the transmittance in a good agreement with the Synchrotron spectra in the entire range of observations for various pressures and optical paths. The region near 100 cm−1 and above appears to be more sensitive to the temperature conditions that should be considered in atmospheric observation for the currently operational and future ground based and space missions.

Monoterpene indole alkaloids from the roots of Alstonia rupestris and their anti-inflammatory activity

Four new monoterpene indole alkaloids (1–4) together with twelve known alkaloids (5–16) were isolated from the roots of Alstonia rupestris. Compound 1 was the first example of C2-symmetric heteroyohimbine-type indole alkaloid homodimer obtained from natural plant resource. Their structures were elucidated on the basis of spectroscopic data. The absolute configuration of 1 was determined by comparison of its calculated and experimental electronic circular dichroism (ECD) spectra. All compounds were evaluated for their anti-inflammatory activities by measuring their NO inhibitory effects in LPS-stimulated RAW 264.7 cells. Compound 2 showed strong NO inhibition with IC50 value of 4.2 ± 1.3 μM. Moreover, compound 2 could decrease the expressions of cyclooxygenase-2 (COX-2) and transforming growth factor beta-1 (TGF-β1).

Isovincathicine from Catharanthus roseus induces apoptosis in A549 cells.

A dimeric indole alkaloid, isovincathicine consisting of an aspidosperma type and modified iboga with C-7-C-20 connection type skeletons was first isolated from Catharanthus roseus, and the structure including stereochemistry was elucidated on the basis of spectroscopic data as well as DP4 statistical analysis. Isovincathicine inhibited cell proliferation in A549 cells. We investigated the detailed mode of action of isovincathicine-induced inhibitory effects on cell proliferation in A549 cells. Flow cytometric analysis showed that isovincathicine-treated cells accumulated in the G2 phase after 24h, and the percentage of cells showing cell death increased after 48h. Western blotting also showed increased expression of BimEL, an apoptosis-related protein, and decreased expression of Mcl-1 and Bcl-xL. Isovincathicine was suggested to induce apoptosis in A549 cells by a mechanism is similar to that of vinblastine.

The NASA Raman spectroscopic database: Ramdb version 1.00

The NASA Raman Spectroscopic Database (Ramdb) was developed to provide a publicly accessible, user-friendly database for spectra relevant to the planetary science community. This paper describes the first set of spectra made available in version 1.00 of Ramdb, the methods used to obtain and process the Raman spectra, and provides a walkthrough of the database website that is located at www.astrochemistry.org/ramdb. Ramdb presently offers 112 laboratory and theoretical Raman spectra of samples relevant to planetary exploration and space science. Laboratory spectra were measured at multiple laser excitation wavelengths, namely: 405, 532, and 785 nm. Spectral data for six projects (amino acids, polycyclic aromatic hydrocarbons, carbon allotropes, minerals, analogs, and planetary studies) are provided as both raw and processed, tagged with key spectroscopic parameters, and, where applicable, accompanied by microscope images of the samples. The contents of Ramdb will be continuously expanded with a wide range of samples relevant to Astrophysics, Planetary Science, Exobiology, and Earth Science, guided by ongoing and future space exploration missions.

LiDB: Database of molecular radiative lifetimes for plasma processes

Abstract LiDB is a newly developed database of molecular vibrational and vibronic state radiative lifetimes. It has been created with the aim of enabling radiative effects to be properly captured in low-temperature plasma models. Datasets have been generated for 36 molecules using comprehensive and highly accurate molecular line lists from the ExoMol spectroscopic database. The main data output of LiDB is radiative lifetimes at vibrational state resolution. Partial lifetimes, which give information on the dominant decay channels in a molecule, are also provided. LiDB is freely available to the scientific community and is hosted at www.exomol.com/lidb. Users can dynamically view molecular datasets or use a specially-designed application programming interface to make data requests. LiDB will continue to expand in the future by adding more molecules, important isotopologues, and neutral and singly-charged atomic species.

2D excitation-emission fluorescence mapping analysis of plant food pigments.

Homogeneous dispersion of plant food pigments is indispensable to study their characteristic fluorescence features for non-destructive rapid monitoring of food systems. However, it is highly challenging to obtain such optical grade homogenized stable dispersion of various plant pigments in aqueous media for tracing their precise fluorescence signatures. Herein, we demonstrate a unique strategy to disperse various pigments, such as chlorophylls, carotenoids and phenolic compounds by the high-speed shear-force mixing of fresh green and red bell peppers (Capsicum annuum) in an aqueous medium with followed centrifugation and filtration. An advanced FLuorescence Excitation-emission (FLE) mapping and optical absorption analysis from the optical grade aqueous bell peppers dispersion allow simultaneous probing of chlorophylls, phenolic compounds and carotenoids by their characteristic electronic transitions. The demonstrated sampling protocols and spectroscopic analysis will be highly beneficial to obtain advanced spectroscopic databases from different food materials for rapid food analysis and quality control.

Polycyclic aromatic hydrocarbon size tracers

ABSTRACT We examine the dependence of polycyclic aromatic hydrocarbon (PAH) band intensity ratios as a function of the average number of carbon atoms and assess their effectiveness as tracers for PAH size, utilizing the data, models, and tools provided by the NASA Ames PAH Infrared Spectroscopic Data base. To achieve this, we used spectra from mixtures of PAHs of different ionization fractions, following a size distribution. Our work, congruent with earlier findings, shows that band ratios that include the 3.3 μm PAH band provide the best PAH size tracers for small-to-intermediate sized PAHs. In addition, we find that band ratios that include the sum of the 15–20 μm PAH features (I$_{\Sigma _{15-20}}$) and the 6.2 or 7.7 μm bands also serve as good tracers for PAH size in the case of small-to-intermediate sized PAHs, for objects under a similar PAH size distribution as with the presented models. For different PAH size distributions, the application of a scaling factor to the I6.2/I$_{\Sigma _{15-20}}$ ratio can provide estimates for the size of the small-to-intermediate PAH population within sources. Employment of the I6.2/I$_{\Sigma _{15-20}}$ and I7.7/I$_{\Sigma _{15-20}}$ ratios can be of particular interest for JWST observations limited only to ∼5–28 μm MIRI(MRS) coverage.

Anti-inflammatory effect of euphane- and tirucallane-type triterpenes isolated from the traditional herb Euphorbia neriifolia L.

The Euphorbiaceae plant Euphorbia neriifolia L. is distributed widely in India, Thailand, Southeastern China, and Taiwan and used as a carminative and expectorant to treat several inflammation-related diseases, such as gonorrhoea, asthma, and cancer. In the course of our search for potential anti-inflammatory agents from the titled plant, 11 triterpenes from the stem of E. neriifolia were isolated and reported in our previous endeavor. Given its rich abundance in triterpenoids, the ethanolic extract in this follow-up exploration has led to the isolation of additional eight triterpenes, including six new euphanes-neritriterpenols H and J-N (1 and 3-7)-one new tirucallane, neritriterpenol I (2), and a known compound, 11-oxo-kansenonol (8). Their chemical structures were elucidated on the basis of spectroscopic data, including 1D- and 2D NMR, and HRESIMS spectra. The absolute stereochemistry of neritriterpenols was determined by single-crystal X-ray diffraction analysis, ICD spectra, and DP4+ NMR data calculations. Compounds 1-8 were also evaluated for their anti-inflammatory activity by using lipopolysaccharide (LPS)-stimulated IL-6 and TNF-α on RAW 264.7 macrophage cells. Intriguingly, the euphane-type triterpenes (1 and 3-8) showed an inhibitory effect on LPS-induced IL-6 but not on TNF-α, while tirucallane-type triterpene 2 showed strong inhibition on both IL-6 and TNF-α.

Excited state dynamics of 1,2,4-triazolyl-thio-pentane-2,4-dione system and their conversion to biologically active novel triazole-S-pyrazole hybrids

The current study focuses on designing and synthesis of novel 1,2,4-triazole appended pyrazoles linked to each other through sulphur atom. Herein we report the condensation of nicotinic hydrazide and isonicotinic hydrazide with aryl isothiocyanate derivatives to obtain carbothioamides which are cyclised to yield 4-aryl-5-(pyridinyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione derivatives under alkaline conditions. Further, condensation of thiones with 3-chloro-pentane-2,4-dione generated novel 1,2,4-triazolyl-thio-pentane-2,4-dione system which was studied for keto-enol tautomerism with the help of spectral data (FT-IR, NMR and Mass). Low energy barrier between three different tautomers (chelated enol, keto, non-chelated enol) resulted in transformation of chelated enol ⇌ non-chelated enol ⇌ keto form upon UV-irradiation. Solvent effects on excited state intramolecular proton transfer (ESIPT) in dione 5a have been studied and the experimental findings were documented with TD-DFT studies. The generated 1,3-diketones were treated with hydrazine hydrate to obtain triazolyl-S-pyrazole hybrids 6. Structure of the synthesized compounds was identified on the basis of spectroscopic data. Single crystal X-ray diffraction (SC-XRD) studies of the representative compound 6a predicts the strong intermolecular hydrogen bonding interaction between N2H2 of pyrazole ring of one molecule and N4 of triazole ring (N2H2…N4) of the other molecule which accounts for the crystal stability. Moreover, triazolyl-S-pyrazole hybrids were also assessed for their antibacterial activities and some derivatives have shown promising activity against E. coli.

Isolation and structure determination of superbcyclin A, a cyclic nonapeptide from Dianthus superbus

To explore the bioactive phytochemical constituents of Dianthus superbus, whole plants of D. superbus were collected and chemically investigated. A rare Caryophyllaceae-type cyclic nonapeptide, named superbcyclin A, was isolated. Its structure was determined on the basis of spectroscopic data and analytical evidence. The absolute configurations of the amino acid residues were identified by advanced Marfey’s analysis.

Diterpenoid alkaloids from Delphinium trichophorum

Three new hetisine type C20-diterpenoid alkaloids, named as trichophorines A–C (1–3), were isolated from Delphinium trichophorum, together with nine known alkaloids (4–12). Their structures were elucidated on the basis of spectroscopic data (1D, 2D NMR, single-crystal X-ray, and HR-ESI-MS). All compounds were evaluated for the inhibitory activities against LPS induced NO production in RAW 264.7 macrophage cells, and none of them showed considerable inhibitory activity.

Cryptadine C, a new C27N3-type Lycopodium alkaloid from Lycopodium cryptomerinum.

A new C27N3-type Lycopodium alkaloid consisting of two decahydroquinolines and a piperidine, cryptadine C (1) was isolated from Lycopodium cryptomerinum. The structure and relative configuration of 1, which is related to those of cryptadines A and B, lycoperine A, and hupercumine A, was elucidated on the basis of spectroscopic data. Cryptadine C showed moderate inhibitory activity against acetylcholinesterase.

Identification of tunnel structures in manganese oxide minerals using micro‐Raman spectroscopy

AbstractManganese oxides have attracted the interest of many researchers due to their broad application field. These oxides possess various electrochemical, adsorption and catalysis properties and are as such applied in the industrial context, for example, steel industry, catalysis and removal of toxins in the ground or in waste water. In the archaeometrical field, manganese oxides have been used as pigments on various artefacts such as pottery and rock art paintings. The diversity of manganese oxide applications highlights the need for a well‐defined Raman spectroscopic database with correct characterization of these compounds. However, identification of manganese oxides by Raman spectroscopy is challenging due to the wide variety of manganese oxides, and manganese oxides are weak Raman scatterers and are susceptible under the laser light. As such, characterization by Raman spectroscopy is not straight forward. In this research, we have focussed on seven natural, mineral (tunnel) samples that were identified by micro‐Raman spectroscopy using two different laser wavelengths (785 and 532 nm). The experimental conditions were controlled to not introduce any modifications (degradation and/or phase transition) of the manganese oxide species. Both lasers have proven to be successful and were able to retrieve well‐characterized Raman spectra for each of the manganese oxide phase, which were compared with published literature.

Interpretable spectroscopic modelling of soil with machine learning

AbstractSpectroscopic modelling of soil has advanced greatly with the development of large spectral libraries, computational resources and statistical modelling. The use of complex statistical and algorithmic tools from the field of machine learning has become popular for predicting properties from their visible, near‐ and mid‐infrared spectra. Many users, however, find it difficult to trust the predictions made with machine learning. We lack interpretation and understanding of how the predictions were made, so that these models are often referred to as black boxes. In this study, I report on the development and application of a model‐independent method for interpreting complex machine learning spectroscopic models. The method relies on Shapley values, a statistical approach originally developed in coalitional game theory. In a case study for predicting the total organic carbon from a large European mid‐infrared spectroscopic database, I fitted a random forest machine learning model and showed how Shapley values can help us understand (i) the average contribution of individual wavenumbers, (ii) the contribution of the spectrum‐specific wavenumbers, and (iii) the average contribution of groups of spectra taken together with similar characteristics. The results show that Shapley values revealed more insights than commonly used interpretation methods based on the variable importance. The most striking spectral regions identified as important contributors to the prediction corresponded to the molecular vibration of organic and inorganic compounds that are known to relate to organic carbon. Shapley values are a useful methodological development that will yield a better understanding and trust of complex machine learning and algorithmic tool in soil spectroscopy research.

Line positions and intensities of the ν1 band of 12CH3I using mid-infrared optical frequency comb Fourier transform spectroscopy

We present a new spectral analysis of the ν1 and ν3+ν1−ν3 bands of 12CH3I around 2971 cm−1 based on a high-resolution spectrum spanning from 2800 cm–1 to 3160 cm–1, measured using an optical frequency comb Fourier transform spectrometer. From this spectrum, we previously assigned the ν4 and ν3+ν4−ν3 bands around 3060 cm–1 using PGOPHER, and the line list was incorporated in the HITRAN database. Here, we treat the two fundamental bands, ν1 and ν4, together with the perturbing states, 2ν2+ν3 and ν2+2ν6±2, as a four-level system connected via Coriolis and Fermi interactions. A similar four-level system is assumed to connect the two ν3+ν1−ν3 and ν3+ν4−ν3 hot bands, which appear due to the population of the low-lying ν3 state at room temperature, with the 2ν2+2ν3 and ν2+ν3+2ν6±2 perturbing states. This spectroscopic treatment provides a good global agreement of the simulated spectra with experiment, and hence accurate line lists and band parameters of the four connected vibrational states in each system. It also allows revisiting the analysis of the ν4 and ν3+ν4−ν3 bands, which were previously treated as separate bands, not connected to their ν1 and ν3+ν1−ν3 counterparts. Overall, we assign 4665 transitions in the fundamental band system, with an average error of 0.00071 cm–1, a factor of two better than earlier work on the ν1 band using conventional Fourier transform infrared spectroscopy. The ν1 band shows hyperfine splitting, resolvable for transitions with J ≤ 2 × K. Finally, the spectral intensities of 65 lines of the ν1 band and 7 lines of the ν3+ν1−ν3 band are reported for the first time using the Voigt line shape as a model in multispectral fitting. The reported line lists and intensities will serve as a reference for high-resolution molecular spectroscopic databases, and as a basis for line selection in future monitoring applications of CH3I.

The inclusion of the MT_CKD water vapor continuum model in the HITRAN molecular spectroscopic database

Atmospheric radiative transfer calculations require information about the spectral absorption properties of all relevant gases in the atmospheric path. For years, much of the atmospheric community has relied on the HITRAN molecular spectroscopic database for absorption line information and the MT_CKD (Mlawer-Tobin_Clough-Kneizys-Davies) water vapor continuum model to specify water vapor continuum absorption. This paper reports on efforts related to the recent inclusion of the MT_CKD water vapor continuum model as a component of HITRAN. Details are provided about the restructuring of the MT_CKD model to separate its code and data and simplify the code structure. We also describe the reformulation of the temperature dependence of the water vapor self continuum in MT_CKD, motivated both by improvements to the model's accuracy at high temperatures and greater consistency with HITRAN. We also briefly describe other recent updates to the MT_CKD water vapor continuum. Finally, perspective is provided on the need for future water vapor continuum measurements.The code and data for the MT_CKD water vapor continuum are available through the HITRAN website at https://hitran.org/mtckd and at the AER GitHub site at https://github.com/AER-RC/MT_CKD_H2O.

Effect of Non-Markovian Collisions on Measured Integrated Line Shapes of CO.

Using cavity ring-down spectroscopy to probe R-branch transitions of CO in N_{2}, we show that the spectral core of the line shapes associated with the first few rotational quantum numbers, J, can be accurately modeled using a sophisticated line profile, provided that a pressure-dependent line area is introduced. This correction vanishes as J increases and is always negligible in CO-He mixtures. The results are supported by molecular dynamics simulations attributing the effect to non-Markovian behavior of collisions at short times. This work has large implications because corrections must be considered for accurate determinations of integrated line intensities, and for spectroscopic databases and radiative transfer codes used for climate predictions and remote sensing.

Expeditious mechanochemical conversion of dihydronaphthalenyl-N-phenylhydrazine-1-carbothioamides into hydrazono-thiazolidin-4-one and hydrazono-dihydrothiazole derivatives—Spectroscopic, DFT, X-ray diffraction, and antibacterial studies

This study reports a facile mechanochemical conversion of N-phenylthiosemicarbazone derivatives of 1-tetralone analogs into thiazolidin-4-ones, thiazolidin-5-ylidene-acetates, and dihydrothiazoles by their condensation with chloroacetic acid, DMAD, and phenacyl bromide, respectively. Triethylammonium hydrogen sulfate [Et3NH]+ [HSO4]− is employed as solid catalyst for this prompt and ecological conversion through which the target products are formed within 10–30 minutes in quantitative yields. The products have been characterized on the basis of spectroscopic data. X-ray diffraction studies of thiazolidin-5-ylidene-acetate 5b, supported by DFT calculations of E/Z isomers of 5b, are presented. Compounds 4, 5, and 7 are assayed for their antibacterial prospects against Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative) bacterial stains. Some derivatives show highly promising antibacterial activities.