Deconvolution Of Spectra Research Articles

Tailoring Photoluminescence Properties of Ternary Zn‐doped Cu─In─Se Quantum Dots via Surfactant Tuning

AbstractThe shape and size‐controlled synthesis of colloidal I−III−VI quantum dots (QDs) can be attained only by a few synthesis strategies via the introduction of various high‐boiling‐point organic surfactants. To further investigate this strategy, in this study, we present a surfactant‐associated controlled synthesis of copper (Cu)‐deficient, zinc (Zn)‐doped Cu─indium (In)─selenium (Se) QDs, followed by a mechanistic investigation of their photophysical properties using surfactants, such as oleylamine (OLA), oleic acid (OA), and diphenylphosphine (DPP). OLA significantly promoted the quantum size effect‐resultant emission wavelength red‐shift, while OA controlled the homogeneous growth of QDs and improved the quantum yields. Moreover, Gaussian deconvolution of the photoluminescence spectra and the bandgap derived from the absorption spectra, by fitting, supported the fact that the radiative transition channels, especially for surface‐trap‐state‐related transitions, are also dependent on the surfactants. Specifically, the conduction band electron‐intragap state transitions and donor‐acceptor transitions were present in all the prepared samples but accounted for different percentages. Furthermore, the surface‐trap‐state‐related transitions significantly faded upon adding (i) OLA/OA as the sole surfactant to the cationic precursor and (ii) the OA + OLA + DPP mixture to the anionic precursor. The findings described here are expected to provide a general strategy for enhancing the tunability of photophysical properties in other QDs systems.

Semi-supervised rotation measure deconvolution and its application to MeerKAT observations of galaxy clusters

Context. Faraday rotation contains information about the magnetic field structure along the line of sight and is an important instrument in the study of cosmic magnetism. Traditional Faraday spectrum deconvolution methods such as RMCLEAN face challenges in resolving complex Faraday dispersion functions and handling large datasets. Aims. We developed a deep learning deconvolution model to enhance the accuracy and efficiency of extracting Faraday rotation measures from radio astronomical data, specifically targeting data from the MeerKAT Galaxy Cluster Legacy Survey (MGCLS). Methods. We used semi-supervised learning, where the model simultaneously recreates the data and minimizes the difference between the output and the true signal of synthetic data. Performance comparisons with RMCLEAN were conducted on simulated as well as real data for the galaxy cluster Abell 3376. Results. Our semi-supervised model is able to recover the Faraday dispersion for extended rotation measure (RM) components, while accounting for bandwidth depolarization, resulting in a higher sensitivity for high-RM signals, given the spectral configuration of MGCLS. Applied to observations of Abell 3376, we find detailed magnetic field structures in the radio relics, and several active galactic nuclei. We also applied our model to MeerKAT data of Abell 85, Abell 168, Abell 194, Abell 3186, and Abell 3667. Conclusions. We have demonstrated the potential of deep learning for improving RM synthesis deconvolution, providing accurate reconstructions at a high computational efficiency. In addition to validating our data against existing polarization maps, we find new and refined features in diffuse sources imaged with MeerKAT.

Tamarind gum based magnesium ion conducting polymer membrane for energy storage applications

A solid bio polymer electrolyte (SPE) based on tamarind gum (TG) and magnesium nitrate was synthesized by a solution casting technique. The amorphous behavior is observed by X-ray diffraction (XRD) analysis, and the degree of crystallinity is calculated from the XRD deconvolution spectra. The interaction between the polymer and the salt was confirmed by Fourier transform infrared (FTIR) analysis. Using FTIR deconvolution spectra, the percentage of free ions can be calculated. The glass transition temperature (Tg) was determined via differential scanning calorimetry (DSC). A higher ionic conductivity (σ) of 1.97 × 10−4 S/cm is observed for the sample with 1 g of tamarind gum and 0.5 g of magnesium nitrate (4 TMN). The conduction mechanism shows that sample 4 TMN obeys the quantum mechanical tunneling model (QMT) at low frequency. The prepared SPEs follow the Arrhenius behavior, and the minimum activation energy (Ea) of 0.207 eV is observed for sample 4 TMN. The lowest relaxation time (τ) was 3.46 × 10−7 s for 4-TMN according to the tangent spectra. The transference number of ions (tion) is calculated by Wagner’s polarization method. The electrochemical stability window observed by linear sweep voltammetry (LSV) is 2.25 V. The primary battery is fabricated by using sample 4TMN, and an open circuit voltage (OCV) of 2.01 V is observed.

Laser-induced fluorescence spectroscopic investigation of Echium amoenum decoction

Herbs containing medicinal ingredients with nutritional value have recently gained attention as an alternative to synthetic drugs. Aside from their pharmaceutical worthiness, a variety of naturally occurring chromophores with specific optical properties have made them valuable sources of natural pigments for many biophotonic applications. Echium Amoenum (EA) is one of the colorful flowers that has been used in traditional medicine for a long time. To our knowledge, although several studies have been carried out on the characterization of EA ingredients and their chemical activities, information on EA fluorescence is still lacking. Here, laser induced fluorescence (LIF) features of the decoction of EA petals were evaluated and found to be highly dependent on the excitation wavelength, EA concentration, and detection geometry. The abundance of pigments, the boundaries of their absorption/emission spectral regions, and the corresponding energy transfer ascertain the contribution of certain chromophores to the cumulative fluorescence activity. Upon deconvolution of the LIF spectra, it was revealed that the different emission bands of rosmarinic acid (corresponding to its dissociated forms) and the luminescent activity of luteolin and β-carotene mainly determine the quantum distribution of the fluorescence of EA. Angular measurement of LIF in a symmetric cylindrical arrangement revealed the presence of the inner filters mainly due to the reabsorption of LIF photons by anthocyanins (flavone, pelargonidin, delphinidin and cyanidin) and carotenoids. We hope that the obtained results will be useful in various fields of photochemistry and biophotonics.

Structure and dynamic viscosity of CaO–SiO2 and CaO–SiO2–B2O3 model slag systems

Correlation dependencies between the dynamic viscosity of slag and its structural parameters were studied to determine an optimal basicity of silicon smelting slag under the addition of boron oxide to eliminate slagging of the bottom of ore-smelting furnaces. Experimental studies were conducted on CaO–SiO2 and CaO– SiO2–B2O3 model slags obtained at 1600°С. Raman spectroscopic analysis was carried out using a Horiba JobinYvon HR800UV analyzer (France). Theoretical calculations of slag viscosity were performed using Urbain and Mills models. During the experiments, the key structural parameters of slag systems varied within the following limits: the experimental Raman spectrum deconvolution function from 1.41 to 2.45 and optical basicity from 0.58 to 0.68. The obtained experimental and theoretical data were related by mathematical dependencies. It was found that the dynamic viscosity of slag can be promptly determined by Raman spectroscopy on the basis of mathematical models. The dependence obtained shows that slag viscosity decreases upon an increase in the number of bridging oxygen atoms in the silicate anion structure. Notably, this decrease in slag viscosity is observed up to the value of the experimental Raman spectrum deconvolution function of ~1.55-1.60 or slag optical basicity of 0.60–0.62. When B2O3 is added, the viscosity undergoes a further decrease. In practice, for CaO–SiO2 slag systems, the use of boroncontaining flux as a liquefying agent is reasonable at CaO/SiO2 = 0.61–0.63 while maintaining the content of B2O3 in the slag at a level of 1%. The two models (classical and modified) proposed by Urbain were established to be more suitable for theoretical calculation of viscosity in CaO–SiO2 and CaO–SiO2–B2O3 systems. Mills’ model is not suitable for these purposes, since the correlation coefficients in the corresponding mathematical model are not sufficiently large. Further research in this direction is required in order to establish appropriate dependencies of slag viscosity on its structural parameters at different temperatures.

Spectroscopic characterization of black N- and P-doped zeolite templated carbons

The incorporation of heteroatoms (X) into the zeolite-templated carbon (ZTC) structure is a widely used technique to tailor its properties for specific applications such as gas adsorption, methane and hydrogen storage, and catalysis. However, the literature lacks sufficient data on Fourier-transform infrared spectroscopy (FTIR) analysis of ZTCs due to the challenge in obtaining high-quality FTIR spectra required for accurate assignment of the C–X bands, primarily caused by the black mass effect. In this work we prepared nitrogen (N) and phosphorus (P) doped ZTC samples using FAU type zeolite as a template and furfuryl alcohol as a carbon precursor. The Raman results confirmed the presence of medium-sized aromatic structures and also showed that doping these structures with N and P leads to some defects, although the overall conformation remains structurally intact. The FTIR spectra of the ZTC materials were obtained by controlling the preparation procedure and humidity, enabling clear analysis of the black samples. A Density Functional Theory (DFT) model based on the dimeric buckybowl structure was developed and complemented by experimental results obtained from X-ray photoelectron spectroscopy (XPS), nuclear magnetic resonance (NMR), and FTIR. The proposed DFT model was then used for deconvolution and precise band assignment of the experimental FTIR spectra. The FTIR deconvolution study also supported the incorporation of N and P into the ZTC as well as the presence of primarily two types of nitrogen species, amide (primary and secondary) and pyridine-like, while P was mainly incorporated as triphenylphosphine oxide and phosphonic acid.

Strategy for improving circular dichroism spectra deconvolution accuracy for macrocyclic peptides in drug discovery

Peptide therapeutics have emerged as an appealing modality in the pharmaceutical industry. Understanding peptide conformation in solution remains one of the most critical areas for peptide drug development. Circular dichroism (CD) spectroscopy is a useful technique to study the secondary structure of proteins and peptides, but the current approaches are limited to protein-focused models to predict high-order structures of peptides, and the models were built based on X-ray crystallography instead of solution-based technique, as a result, such models may have poor predictions for peptides. In this study, we present a novel CD deconvolution model to determine peptide conformation in solution. To quantitatively obtain secondary structure information using CD, a calibration model is needed beforehand to establish the relationship between each secondary structure feature and the corresponding CD response. A reference set containing the majority of cyclic peptides with known structures from solution-state NMR spectroscopy was used to build the calibration model for CD deconvolution. Improved prediction accuracy on the secondary structure determination for cyclic peptides was achieved by this model compared to the commercial standard model using commercially available platforms. This new CD deconvolution method is crucial for peptide conformational analysis in solution, and has the potential to greatly accelerate peptide drug candidate optimization in the pharmaceutical drug discovery field.

Analysis of the Structure of 14 Therapeutic Antibodies Using Circular Dichroism Spectroscopy.

Understanding the impact of the manufacturing environment on therapeutic monoclonal antibody (mAb) structures requires new process analytical technology. Here, we describe the creation of a new reference set for the circular dichroism (CD) spectra of mAbs. Data sets of the highest quality were collected by synchrotron radiation CD for 14 different mAbs in both native and acid-stressed states. Deconvolution of far-UV spectra for the mAb cohort identified two current reference sets (SP175 and SMP180) as assigning accurate secondary structures, irrespective of the analysis program employed. Scrutiny of spectra revealed significant variation in the far-UV and especially near-UV CD of the 14 mAbs. Two spectral features were found to be sensitive to changes in solution pH, i.e., the far-UV positive peak at 201-202 nm and the near-UV negative exciton couplet around 230-240 nm. The latter feature offers attractive possibilities for in-line CD-based monitoring of the mAb structure during manufacture.

Computed Tomography and Fluorescence Spectroscopy Blood Plasma Analysis Study for Kynurenic Acid as a Diagnostic Approach to Chronic Coenurosis in Sheep.

Coenurosis is a parasitic disease caused by the larval stage of Taenia multiceps, Coenurus cerebralis, typically found in the central nervous system of different livestock such as sheep and goats. The blood plasma from fifteen clinically healthy sheep and six sheep with neurological symptoms was studied by fluorescence spectroscopy in order to establish the contribution of kynurenic acid (KYNA), the neuroprotective metabolite of the kynurenine pathway, to the total fluorescence of the plasma. CT scans were used to confirm the presence of cysts in the central nervous system of sheep with neurological symptoms. The fluorescence spectroscopy analysis and further spectra deconvolution process revealed some significantly lower KYNA contributions to the total plasma fluorescence in sheep with coenurosis compared to healthy controls. Our results indicate that KYNA emission parameters could serve as valuable diagnostic markers, particularly for detecting preclinical cases of coenurosis, thus allowing for improved farm management practices.

NMR-Onion - a transparent multi-model based 1D NMR deconvolution algorithm

We introduce NMR-Onion, an open-source, computationally efficient algorithm based on Python and PyTorch, designed to facilitate the automatic deconvolution of 1D NMR spectra. NMR-Onion features two innovative time-domain models capable of handling asymmetric non-Lorentzian line shapes. Its core components for resolution-enhanced peak detection and digital filtering of user-specified key regions ensure precise peak prediction and efficient computation. The NMR-Onion framework includes three built-in statistical models, with automatic selection via the BIC criterion. Additionally, NMR-Onion assesses the repeatability of results by evaluating post-modeling uncertainty. Using the NMR-Onion algorithm helps to minimize excessive peak detection.

High-resolution quadrupole improves spectral purity and reduces interference from non-target ions in isobaric multiplexed quantitative proteomics

BackgroundMass spectrometry (MS)-based proteomics is a powerful tool for identifying and quantifying proteins. However, chimeric spectra caused by the fragmentation of multiple precursors within the same isolation window impair the accuracy of peptide identification and isobaric mass tag-based quantification. While there have been advances in computational deconvolution of chimeric spectra and methods to further separate the peptides by ion mobility or through MSn, the use of narrower isolation windows to decrease the fraction of chimeric species remains to be fully explored. ResultsWe present results obtained on a SCIEX TripleTOF instrument where the quadrupole was optimized and tuned for precursor isolation at 0.1 Da (FWHH). Using a three-proteome model (trypsin digest of protein lysates from yeast, human and E. coli) and 8-plex iTRAQ labeling to document the interference effect, we investigated the impact of co-fragmentation on spectral purity, identification accuracy and quantification accuracy. The narrow quadrupole isolation window significantly improved the spectral purity and reduced the interference of non-target precursors on quantification accuracy. The high-resolution isolation strategy also reduced the number of false identifications caused by chimeric spectra. While these improvements came at the cost of sensitivity loss, combining high-resolution isolation with other advanced techniques, including ion mobility, may result in improved accuracy in identification and quantification. SignificanceCompared to standard-resolution quadrupole isolation (0.7 Da), high-resolution quadrupole isolation (0.1 Da) significantly improved the spectral purity and quantification accuracy while reducing the number of potential false identifications caused by chimeric spectra, thus showing excellent potential for further development to analyze clinical proteomics samples, for which high accuracy is essential.

Structural, thermal and X-ray photoelectron spectroscopic properties of boro-tellurite based quaternary glass system

The structural, functional and thermal properties of the TeZnCaB glass system were investigated in this work. The thermal properties of the glass system were studied using DSC (differential scanning calorimetry), and the glass transition temperature (Tg) decreased from 470 °C to 438 °C with increasing TeO2 concentration. The vibrational and bending modes of the TeZnCaB glass samples were depicted by Raman spectroscopy analysis. FTIR (Fourier-transform infrared spectroscopy) was performed to investigate the functional groups of TeO2 and B2O3 in the samples. The TeZnCaB glass samples consist of TeO3, TeO4, BO4 and BO3 structural units. XPS (X-ray photoelectron spectroscopy) was investigated to reveal information about the chemical environment and the creation of NBO (non-bridging oxygen) and BO (bridging oxygen) for the different glass systems. The high-resolution Te3d spectrum confirms the presence of various tellurium-based structural units such as TeO4, TeO3, and TeO3+1. The deconvolution of B1s spectra confirmed the existence of two forms of boron (B) such as BO4 (four coordination) and BO3 (three coordination) in the TeZnCaB glass system.

Ultrasound-assisted hydrolysis of food waste using glucoamylase: Statistical optimization and mechanistic analysis with molecular simulations

This paper reports investigations in food waste hydrolysis using ternary approach that combines statistical optimization, ultrasound-assisted enhancement of hydrolysis kinetics, and molecular simulations that provide physical insight into the process. Initial optimization of hydrolysis parameters (Box–Behnken design) resulted in total reducing sugar yield of 263.4 mg/g biomass in 42 h. Sonication of hydrolysis mixture at 35 kHz at 20 % duty cycle yielded 4× reduction in hydrolysis time with 22 % enhancement in TRS yield (320 mg/g biomass). Analysis of GLCM's secondary structure through FTIR spectra deconvolution revealed significant changes induced by sonication. Sonication led to reduction in α-helix, and increase in random coil content. Molecular dynamics simulations unveiled majority of amino acid residues associated with GLCM binding pocket in α-helix and random coil regions. Consequently, sonication widened the binding pockets, facilitating easier transport of substrate and product. This effect translated into faster kinetics of enzymatic food waste hydrolysis.

Liquid Binary and Ternary Electrolytes Mixtures for Low-Temperature Sulfurized Carbon Batteries

Active sulfurized carbon (SC) has been proposed as promising alternative to enable sulfur as the next generation cathode material due its ability to confine sulfur and suppresses polysulfide shuttling. Pragmatic cell performance of SC electrodes needs to extend over a wide range of temperatures from -20 °C to 60 °C. Low-temperature performance of SC cells is mainly limited by electrolyte wettability, ionic mobility between the electrodes, and the nature of the formed solid electrolyte interphase. In this work we have utilized electrolyte binary and ternary mixtures based on carbonates, ethers, and fluorinated solvents to enhance the SC cell discharge performance up to -20 °C. To understand the effects of electrolyte mixtures in the cell performance we have utilized electrochemical impedance spectroscopy (EIS) as a function of temperature and voltage. The lower cell resistance translates into a higher rate capability, cyclability, and low-temperature performance. Based on the EIS response and its spectra deconvolution we proposed an apparent electrical equivalent circuit that permits the elucidation of resistance elements and their magnitude such as the ohmic, electron charge transfer, surface film, and mass transport resistance to provide a phenomenological understanding on how the mixtures can enhance the electrochemical performance. Furthermore, differential capacity analysis and Hybrid Pulse Power Characterization (HPPC), are utilized to support the characterization. Finally, best performance electrolyte mixtures were utilized to build >0.5 Ah pouch cells for testing at low temperatures, discharge rates, and pressure conditions.

(Invited) Consideration on Gate Stack Formation Processes of Ultrawide Bandgap Ga2O3 with SiO2 Dielectric Layer

MOSFETs on β-Ga2O3 are expected to be a high-efficient and cost-effective alternative option of high-voltage power devices. Taking account of the reliability and the large conduction-band offset against β-Ga2O3, it would be reasonable to employ SiO2 as the gate dieletric. In this study we investigated the effects of post-deposition annealing (PDA) on SiO2/β-Ga2O3 MOS gate stacks, in terms of the MOS electrical characteristics and the band alignment.β-Ga2O3 (001) wafers with ~2×1016 cm-3 n-type doped epitaxial layers were cleaned in diluted HF solution, and SiO2 films were deposited by electron-beam (EB) evaporation of Si in O2 ambient of ~1×10-2 Pa, followed by PDA at various temperatures from 600 to 1000℃ in either O2 or N2 ambient. Au was evaporated as gate electrode to form MOS capacitors. X-ray photoelectron spectroscopy (XPS) was conducted on the stacks with ~3nm-thick SiO2 for the evaluation of band alignment. Ultraviolet photoelectron spectroscopy (UPS) was also employed to determine the band diagram of β-Ga2O3 (001).Nearly-ideal capacitance-voltage characteristics were obtained for the MOS capacitor fabricated with O2-PDA at 1000℃. The interface state density (Dit) determined by conductance method decreased down to ~1010 cm-3 at the energy level of EC−0.2 eV by PDA at higher temperature. The hysteresis width (ΔVhys) of C-V curves was smaller for the samples annealed at higher temperatures. The flatband voltage (VFB) shift after O2-PDA resulted in VFB close to the ideal value estimated from the physical properties of Au and Ga2O3, suggesting that fixed charge density at the interface would be minimized. However, PDA in N2 at 1000℃ resulted in a negative shift of VFB, which indicates the formation of positive fixed charges in the stack. The beneficial influences of O2-PDA on those characteristics suggest that an oxygen deficiency introduced near the interface is one of the origins of interface defect states. It is noteworthy that Ga3d XPS on the surface of Ga2O3 substrate always shows a tailing in lower binding energy side, which is indicating oxygen deficiency on the surface. The intensity of this lower-binding-energy component reduced significantly when a bare-Ga2O3 substate was annealed in O2, however, it did not decrease efficiently even after O2-PDA when the surface was covered with SiO2. This is probably due to the oxygen rearrangement at SiO2/Ga2O3 interface determined by the difference of material properties of those oxides. This fact suggests that the Ga2O3 surface easily forms oxygen vacancies when it is covered with SiO2. This would be the reason why the formation of interface defect states is not suppressed without O2-PDA.Next the band diagram of β-Ga2O3 (001) substrate was investigated by UPS analysis where the energy level of valence band edge referring to the vacuum level was evaluted from the energy difference between minimum (cut-off) and maximum edges of the obtained kinetic energy spectra of photoelectrons. As a result we found the valence band edge of of β-Ga2O3 (001) was ~8.2 eV below the vacuum level, where the influences of O2 annealing at 1000℃ on the valence band edge energy level was limited to the shift within ~0.1eV. This would tell us the valence band offset between SiO2 and Ga2O3 should be around ~1.1eV, and the conduction band offset between them is to be around 2.8-2.9eV, by taking account of the well-reported SiO2 band diagram and assuming the bandgap of β-Ga2O3 as 4.7eV. On the other hand, the valence band offset estimated from the deconvolution of the XPS valence band spectrum for a ~3nm-thick SiO2/β-Ga2O3 stack from the energy edge difference between the deconvoluted spectra corresponding to SiO2 and Ga2O3, was a few hundreds of mV smaller than the above expected value (~1.1eV). This discrepancy is indicating the formation of an interface dipole layer between SiO2 and Ga2O3 with a pair of nagative and positive charges aligned at the interface to cause a shift in the band alignment. The magnitude of such dipole was indicated to be more significant (~0.5eV) for the stack after PDA at 1000℃, whereas it was less (0.2~0.3eV) after PDA at 600℃.In conclusion, we demonstrated that SiO2/β-Ga2O3 (001) MOS capacitors showed nearly-ideal electrical characteristics with significantly reduced interface defect density and small fixed charge density by applying O2-PDA. The band alignment of SiO2/β-Ga2O3 (001) MOS stack was clarified by photoelectron spectroscopy to confirm a very large conduction band offset of the stack, but an influence of the formation of interface dipole layer between SiO2 and Ga2O3 on the band alighment was also indicated.

Non-Target Screening of Chemicals in Selected Cotton Products by GC/MS and Their Safety Assessment.

Cotton is used for the production of textiles, hygiene and cosmetic materials. During cultivation and technological processes, various types of substances (surfactants, softeners, lubricants, etc.) penetrate cotton, which can have a harmful effect on both the human body and the environment. The aim of this study was to analyze selected cotton products in order to identify the substances contained and to describe the potential possibilities of inducing textile contact dermatitis (CD). The impact of the identified compounds on the aquatic environment was also taken into account. Nine samples of cotton clothing and seven samples of cotton pads from various manufacturers were tested. Samples after extraction using the FUSLE (Focused Ultrasonic Liquid Extraction) technique were analyzed with GC/MS. Qualitative analysis was based on comparing mass spectra with library spectra using the following mass spectra deconvolution programs: MassHunter (Agilent), AMDIS (NIST), and PARADISE (University of Copenhagen). The parameter confirming the identification of the substance was the retention index. Through the non-target screening process, a total of 36 substances were identified, with an average AMDIS match factor of approximately 900 ("excellent match"). Analyzing the properties of the identified compounds, it can be concluded that most of them have potential properties that can cause CD, also due to the relatively high content in samples. This applies primarily to long-chain alkanes (C25-C31), saturated fatty acids, fatty alcohols (e.g., oleyl alcohol), and fatty acid amides (e.g., oleamide). However, there are not many reports describing cases of cotton CD. Information on the identified groups of compounds may be helpful in the case of unexplained sources of sensitization when the skin comes into contact with cotton materials. Some of the identified compounds are also classified as dangerous for aquatic organisms, especially if they can be released during laundering.

FREE: Enhanced Feature Representation for Isotopic Envelope Evaluation in Top-Down Mass Spectra Deconvolution.

The aim of deconvolution of top-down mass spectra is to recognize monoisotopic peaks from the experimental envelopes in raw mass spectra. So accurate assessment of similarity between theoretical and experimental envelopes is a critical step in mass spectra data deconvolution. Existing evaluation methods primarily rely on intensity differences and m/z similarity, potentially lacking a comprehensive assessment. To overcome this constraint and facilitate a comprehensive and refined assessment of the similarity between theoretical and experimental envelopes, there exists an imperative to systematically explore and identify increasingly efficacious features for assessing this correspondence. We present enhanced feature representation for isotopic envelope evaluation (FREE) that derives diverse feature representations, encapsulating fundamental physical attributes of envelopes, including peak intensity and envelope shape. We trained FREE and evaluated its performance on both the ovarian tumor (OT) (human OT cells) data set and zebrafish (ZF) (brain in mature female ZF) data set. Specifically, comparing the state-of-art method, FREE demonstrates higher performance in multiple evaluation metrics across both the OT and ZF data sets, with a particular emphasis on precision, and it demonstrates accurate predictions of a greater number of positive envelopes among the top-ranked envelopes based on their scores. Moreover, within a cross-species data set of ZF, FREE identified a higher number of proteoform-spectrum matches (PrSMs), increasing the count from 50,795 to 52,927 compared to EnvCNN, the amalgamation of FREE with TopFD also exhibits a commendable capacity to discern 117,883 fragment ions, thus surpassing the 97,554 fragment ions identified through the application of EnvCNN in conjunction with TopFD. To further validate the performance of FREE, we have tested 10 a cross-species top-down proteomes containing 36 subdata set from ProteomeXchange. The results reveal that, after deconvolution with TopFD + FREE, TopPIC identifies more PrSMs across these 10 data sets in both the first and second rounds of experiments. These findings underscore the robustness and generalization capabilities of the FREE approach in diverse proteomes.

Impact of Rare Sugar D-Allulose on Hardening of Starch Gels during Refrigerated Storage.

The rare sugar D-allulose (Alu), with ca. 10% calories of sucrose (Suc), is a promising alternative sugar that can be used to improve the quality of starch gels in storage. The effects of Alu (compared to Suc) on the hardening and microstructural and molecular order of amylopectin-rich (glutinous rice (GR) and corn amylopectin (CAP)) and amylose-rich (corn (C)) starch gels were investigated. Alu and Suc both suppressed hardening in C gels, while Alu but not Suc was effective in GR and CAP gels. SEM results showed that Alu-containing GR and CAP maintained a relatively large pore size compared to Suc-containing gels. The deconvolution of FTIR spectra revealed that Alu-containing GR and CAP gels had lower ratios of intermolecular hydrogen bonds and higher ratios of loose hydrogen bonds than Suc-containing gels. For amylose-rich C gels, on the other hand, such tendencies were not observed. The influence of Alu on amylopectin-rich gels could be because Alu reduced the ratio of intermolecular hydrogen bonds, which might be involved in amylopectin recrystallization, and increased that of loose hydrogen bonds. The results suggest that Alu is more effective than Suc in inhibiting the hardening of amylopectin-rich starch gels during refrigerated storage.

Impact of the spatial structure of alkyl chains on properties of thiophene-substituted diketopyrrolopyrroles: Part II – Spectroscopic study

The study concerns the impact of a difference in geometry of the side alkyl chains of oligothiophene derivatives of diketopyrrolopyrrole (DPP) on their spectroscopic properties and aggregation in solutions, in Langmuir layers, and thin films. Using a combination of theoretical and experimental approaches, this study aims to explain the aggregating behaviour of thiophene-substituted DPP derivatives. Various methods were used to characterise the dyes, including absorption spectroscopy also with polarized light, fluorescence spectroscopy, Langmuir techniques, and time-dependent density functional theory (TD-DFT) calculations. The presented results emphasise a significant impact of side alkyl chains on DPP's molecular behaviour, notably evident in thin-layer structures. Interestingly, the deconvolution of the absorption spectra revealed three bands in the red region. Insightful analysis of temperature-dependent absorption, excitation, and emission fluorescence spectra indicates the co-existence of monomer, dimer, and a higher aggregate forms, most likely a tetrameric structures. Moreover, such a complexity of molecular organisation of dyes appears already in the solution. Differences in spectral properties of the dyes studied are robustly visible in changes in the spectra of the air–water interface, where the dye with the branched side group changes the mutual orientation in dimeric structures, leading to the formation of H-type aggregates, which was observed as an almost 20-nm spectral blue shift during Langmuir layer compression. The results presented highlight the need for care in interpretation of the intensity ratio of DPP spectra and spectral shift as the sole determinants of the aggregation state.

Individual quantification of ozone and reactive nitrogen species in mixtures by broadband UV–visible absorption spectra deconvolution

Ozone (O3), nitrogen oxides (NO x ), and reactive nitrogen species (RNS) play critical roles in atmospheric-pressure plasma applications. Although it is crucial to individually quantify these species to understand atmospheric-pressure plasmas and increase their effectiveness, the lack of reliable and cost-effective diagnostics makes this difficult for many researchers. To address this problem, we introduce a new deconvolution method of broadband ultraviolet–visible absorption spectra for the simultaneous measurement of eight species—O3, NO, NO2, NO3, N2O4, N2O5, HONO, and HNO3. Processing of broadband spectra enables deconvolution of similar cross-section profiles and measurement of high densities exceeding the instrumental limit. Novel correction processes enable accurate analysis despite incomplete cross-section data and utilize a priori chemical knowledge to ensure theoretically reasonable results. Two case studies test the efficacy of the method: NO2 and N2O4 equilibria, and reactive species produced by a surface dielectric barrier discharge. With an analysis time of 15–20 ms per spectrum, the measured densities agree well with other theoretical and experimental results, and detection limits on the order of ppmv were achieved with a short path length of 15 cm. This spectral analysis method will facilitate the real-time monitoring of O3, NO x , and RNS in many scientific research and industrial applications of atmospheric pressure plasmas.