Explainable artificial intelligence for spectroscopy data: a review.

Explainable artificial intelligence (XAI) has gained significant attention in various domains, including natural and medical image analysis. However, its application in spectroscopy remains relatively unexplored. This systematic review aims to fill this gap by providing a comprehensive overview of the current landscape of XAI in spectroscopy and identifying potential benefits and challenges associated with its implementation. Following the PRISMA guideline 2020, we conducted a systematic search across major journal databases, resulting in 259 initial search results. After removing duplicates and applying inclusion and exclusion criteria, 21 scientific studies were included in this review. Notably, most of the studies focused on using XAI methods for spectral data analysis, emphasizing identifying significant spectral bands rather than specific intensity peaks. Among the most utilized AI techniques were SHapley Additive exPlanations (SHAP), masking methods inspired by Local Interpretable Model-agnostic Explanations (LIME), and Class Activation Mapping (CAM). These methods were favored due to their model-agnostic nature and ease of use, enabling interpretable explanations without modifying the original models. Future research should propose new methods and explore the adaptation of other XAI employed in other domains to better suit the unique characteristics of spectroscopic data.

Biosynthesis of carotenoids in Azospirillum brasilense Cd is mediated via squalene (C30) route.

Azospirillum brasilense is a non-photosynthetic α-Proteobacteria, belongs to the family of Rhodospirillaceae and produces carotenoids to protect itself from photooxidative stress. In this study, we have used Resonance Raman Spectra to show similarity of bacterioruberins of Halobacterium salinarum to that of A. brasilense Cd. To navigate the role of genes involved in carotenoid biosynthesis, we used mutational analysis to inactivate putative genes predicted to be involved in carotenoid biosynthesis in A. brasilense Cd. We have shown that HpnCED enzymes are involved in the biosynthesis of squalene (C30), which is required for the synthesis of carotenoids in A. brasilense Cd. We also found that CrtI and CrtP desaturases were involved in the transformation of colorless squalene into the pink-pigmented carotenoids. This study elucidates role of some genes which constitute very pivotal role in biosynthetic pathway of carotenoid in A. brasilense Cd.

Negative Thermal Expansion in ABC(MoO4)3 Compounds.

Negative thermal expansion (NTE) compounds provide a solution for the mismatch of coefficients of thermal expansion in highly integrated device design. However, the current NTE compounds are rare, and how to effectively design new NTE compounds is still challenging. Here, a new concept is proposed to design NTE compounds, that is, to increase the flexibility of framework structure by expanding the space in framework structure compounds. Taking the parent compound NaZr2(PO4)3 as a case, a new NTE system AIBIICIII(MoO4)3 (A = Li, Na, K, and Rb; B = Mg and Mn; C = Sc, In, and Lu) is designed. In these compounds, the large volume of MoO4 tetrahedron is used to replace the small volume of PO4 tetrahedron in NaZr2(PO4)3 to enhance structural space and NTE performance. Simultaneously, a joint study of temperature-dependent X-ray diffraction, Raman spectroscopy, and the first principles calculation reveals that the NTE in AIBIICIII(MoO4)3 series compounds arise from the coupled oscillation of polyhedral. Large-radius ions are conducive to enhancing the space and softening the framework structure to achieve the enhancement of NTE. The current strategy for designing NTE compounds is expected to be adopted in other compounds to obtain more NTE compounds.

Deep-Ultraviolet and Helicity-Dependent Raman Spectroscopy for Carbon Nanotubes and 2D Materials.

Recent progress of Raman spectroscopy on carbon nanotubes and 2D materials is reviewed as a topical review. The Raman tensor with complex values is related to the chiral 1D/2D materials without mirror symmetry for the mirror in the propagating direction of light, such as chiral carbon nanotube and black phosphorus. The phenomenon of complex Raman tensor is observed by the asymmetric polar plot of helicity-dependent Raman spectroscopy using incident circularly-polarized lights. First-principles calculations of resonant Raman spectra directly give the complex Raman tensor that explains helicity-dependent Raman spectra and laser-energy-dependent relative intensities of Raman spectra. In deep-ultraviolet (DUV) Raman spectroscopy with 266 nm laser, since the energy of the photon is large compared with the energy gap, the first-order and double resonant Raman processes occur in general k points in the Brillouin zone. First-principles calculation is necessary to understand the DUV Raman spectra and the origin of double-resonance Raman spectra. Asymmetric line shapes appear for the G band of graphene for 266 nm laser and in-plane Raman mode of WS2 for 532 nm laser, while these spectra show symmetric line shapes for other laser excitation. The interference effect on the asymmetric line shape is discussed by fitting the spectra to the Breit-Wigner-Fano line shapes.

Triflate's bigger brother: The unprecedented tribrate anion, [Br3 CSO3 ].

The synthesis of the unprecedented [Br3 CSO3 ]- anion starts with the bromination of phenylmethanesulfonate, C6 H5 OSO2 CH3 , with KOBr leading to C6 H5 OSO2 CBr3 . The formation of the [CBr3 ] moiety has been proved, also by an X-ray structure determination of the compound (triclinic, P-1, a=685.9(2), b=698.1(2), c=1190.2(3) pm, α=93.99(1)°, ß=97.42(1)°, γ=94.45(1)°). The ester C6 H5 OSO2 CBr3 can be split under basic conditions. The resulting acid provides access to the yet unknown tribromomethanesulfates ("tribrates"). K[Br3 CSO3 ] ⋅ H2 O, the first tribrate known so far has been characterized comprehensively, including an X-ray structure determination (monoclinic, C2/c, a=2267.1(2), b=1282.25(8), c=2618.2(2) pm, ß=111.266(2)°), vibrational spectroscopy and theoretical calculations. Moreover, the thermal analysis shows that, after loss of the crystal water, the tribrate decomposes between 530 and 630 K.

Angle-Dependent Raman Spectra of Crystal Polymorphs of GaO: A Computational Study.

Two crystal polymorphs of GaO consisting of GaO-H and GaO-T monolayers are proposed in this study. Based on the density functional theory calculations, the phonon dispersion demonstrates that both GaO-H and GaO-T monolayers could be stable. The band gaps of GaO-H and GaO-T monolayers are 1.51 and 1.43 eV, respectively. When an external electric field is applied, the band gaps of GaO monolayers are reduced dramatically, down to 0.13 eV with the field of 0.7 V/Å. Because of the decreased symmetry of C3v under an external electric field, more peaks of Raman spectra can be obtained. The angle-dependent Raman spectra of A ' 1 1 ${{\rm{A}}{{^\prime}}_1^1 }$ and A ' 1 2 ${{\rm{A}}{{^\prime}}_1^2 }$ of GaO-H monolayer, and A 1 g 1 ${{\rm{A}}_{1{\rm{g}}}^1 }$ and A 1 g 2 ${{\rm{A}}_{1{\rm{g}}}^2 }$ of GaO-T monolayer are discussed seperately, with the incident lasers of 488 and 532 nm. Additionally, the Raman intensity distribution shows that the incident light should be parallel to the plane of the GaO monolayer to obtain more comparable Raman spectra. These investigations of the crystal polymorphs of GaO monolayers may guide the experimental investigations of GaO monolayers and potential optoelectronic applications.

Adsorption Structures, Vibrational Raman Spectra and Chemical Binding Properties of Thioglycolic Acid on Cu(111) Surfaces: A DFT Study.

Copper is widely used in everyday life and industrial production because of its good electrical and thermal conductivity. To overcome copper oxidation and maintain its good physical properties, small organic molecules adsorbed on the surface of copper make a passivated layer to further avoid copper corrosion. In this work, we have investigated thioglycolic acid (TGA, another name is mercaptoacetic acid) adsorbed on copper surfaces by using density functional theory (DFT) calculations and a periodical slab model. We first get five stable adsorption structures, and the binding interaction between TGA and Cu(111) surfaces by using density of states (DOS), indicating that the most stable configuration adopts a triple-end binding model. Then, we analyze the vibrational Raman spectra of TGA adsorbed on the Cu(111) surface and make vibrational assignments according to the vibrational vectors. Finally, we explore the temperature effect of the thermodynamically Gibbs free energy of TGA on the Cu(111) surface and the antioxidant ability of the small organic molecular layer of copper oxidation on the copper surface. Our calculated results further provide evidences to interpret the stability of adsorption structures and antioxidant properties of copper.

Modification of WS2thin film properties using high dose gamma irradiation.

The tunability of the transition metal dichalcogenide properties has gained attention from numerous researchers due to their wide application in various fields including quantum technology. In the present work, WS2has been deposited on fluorine doped tin oxide substrate and its properties have been studied systematically. These samples were irradiated using gamma radiation for various doses, and the effect on structural, morphological, optical and electrical properties has been reported. The crystallinity of the material is observed to be decreased, and the results are well supported by x-ray diffraction, Raman spectroscopy techniques. The increase in grain boundaries has been supported by the agglomeration observed in the scanning electron microscopy micrographs. The XPS results of WS2after gamma irradiation show evolution of oxygen, carbon, C=O, W-O and SO4-2peaks, confirming the addition of impurities and formation of point defect. The gamma irradiation creates point defects, and their density increases considerably with increasing gamma dosage. These defects crucially altered the structural, optical and electrical properties of the material. The reduction in the optical band gap with increased gamma irradiation is evident from the absorption spectra and respective Tauc plots. TheI-Vgraphs show a 1000-fold increase in the saturation current after 100 kGy gamma irradiation dose. This work has explored the gamma irradiation effect on the WS2and suggests substantial modification in the material and enhancement in electrical properties.

A shifted ratio spectrum strategy for effective subtraction of fluorescence interference in Raman spectra.

Raman spectroscopy is an important technique for analyzing the chemical composition of samples in many fields. A severe challenge often encountered in Raman measurements is the presence of a concurrent fluorescence background, especially in biological samples. In order to obtain accurate Raman spectra, the fluorescence background must be subtracted from the original Raman spectra. We proposed a shifted ratio spectrum method to subtract the strong fluorescence background from the original Raman spectrum. First, the original Raman spectrum is divided into multiple regions according to the spectral shape of the shifted ratio spectra, and then, Gaussian fitting is performed in each region. The fitting results are stitched together in order to obtain the complete fluorescence background. Finally, this fluorescence background is subtracted from the original spectrum to obtain a pure Raman spectrum. This method can accurately subtract the fluorescence background of Rhodamine 6G (R6G)/ethanol solution and serum. This highlights the great potential of this method for applications in both biological and non-biological samples.

Exploring the Influence of Morphology on Bipolaron-Polaron Ratios and Conductivity in Polypyrrole in the Presence of Surfactants.

This research aims to deepen the understanding of the relationship between conductivity and morphology in polypyrrole (PPy) via a comparison of the bipolaron to polaron ratios with a focus on the C-H deformation area. PPy samples were synthesized with different surfactants: sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB), and tween 80 (TW). This study revealed that SDS significantly altered the bipolaron and polaron in the C-H deformation region and showed higher conductivity than other surfactants. Notably, the morphological shifts to a sheet-like structure when using ammonium sulfate (APS) contrasted with the particle-like form observed with ferric chloride (FeCl3). These results showed that if the oxidant changed, the bipolaron and polaron ratios in C-H deformation were unrelated to PPy morphology. However, this work showed a consistent relationship between SDS use, the bipolaron and polaron ratios in the C-H deformation, and the conductivity properties. Moreover, the natural positive charge of PPy and negatively charged SDS molecules may lead to an electrostatic interaction between PPy and SDS. This work assumes that this interaction might cause the transformation of polaron to bipolaron in the C-H deformation region, resulting in improved conductivity of PPy. This work offers more support for the future investigation of PPy characteristics.

Material and Microstructure Analysis of Wood Color Paintings from Shaanxi Cangjie Temple, China.

Cangjie Temple was built to commemorate Cangjie, the legendary inventor of Chinese characters. It stands as one of the few remaining temples in China dedicated to the invention and creation of writing. In this study, the material properties of wooden paintings from the Cangjie temple were characterized using Polarized Light Microscopy (PLM), Scanning Electron Microscopy coupled with Energy Dispersive X-ray Spectroscopy (SEM-EDS), Micro-confocal Raman Spectroscopy, X-ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), and Pyrolysis-Gas Chromatography-Mass Spectrometry (Py-GC/MS). It was confirmed that the pigments of the paintings included cinnabar, lapis lazuli, lead white, Paris green, and carbon black. The proteinaceous glue was used as an adhesive in the pigment samples, with tung oil likely being utilized as a primer for the wooden structures before painting. This study not only provides valuable data support for the conservation and restoration of the architectural features of Cangjie Temple but also provides useful reference for the maintenance and inheritance of similar ancient buildings.

Quantum Chemical Investigation into the Structural Analysis and Calculated Raman Spectra of Amylose Modeled with Linked Glucose Molecules.

This study presents a quantum chemical investigation into the structural analysis and calculated Raman spectra of modeled amylose with varying units of linked glucose molecules. We systematically examined the rotation of hydroxymethyl groups and intramolecular hydrogen bonds within these amylose models. Our study found that as the number of linked glucose units increases, the linear structure becomes more complex, resulting in curled, cyclic, or helical structures facilitated by establishing various intramolecular interactions. The hydroxymethyl groups were confirmed to form interactions with oxygen atoms and with hydroxymethyl and hydroxyl groups from adjacent rings in the molecular structures. We identified distinct peaks and selected specific bands applicable in various analytical contexts by comparing their calculated Raman spectra. Representative vibrational modes within selected regions were identified across the different lengths of amylose models, serving as characteristic signatures for linear and more coiled structural conformations. Our findings contribute to a deeper understanding of amylose structures and spectroscopic signatures, with implications for theoretical studies and potential applications. This work provides valuable reference points for the detailed assignment of Raman peaks of amylose structure, facilitating their application in broader research on carbohydrate structures and their associated spectroscopic properties.

Extra-High Mechanical and Phononic Anisotropy in Black Phosphorus Blisters.

Strain is an effective strategy to modulate the electrical, optical, and optoelectronic properties of 2D materials. Conventional circular blisters could generate a biaxial stretching of 2D membranes with notable strain gradients along the hoop direction. However, such a deformation mode cannot be utilized to investigate mechanical responses of in-plane anisotropic 2D materials, for example, black phosphorus (BP), due to its crystallographic orientation dependence. Here, a novel rectangular-shaped bulge device is developed to uniaxially stretch the membrane, and further provide a promising platform to detect orientation-dependent mechanical and optical properties of anisotropic 2D materials. Impressively, the derived anisotropic ratio of Young's modulus of BP flakes is much higher than the values obtained via the nanoindentation method. The extra-high strain-dependent phononic anisotropy in Raman modes along different crystalline orientations is also observed. The designed rectangular budge device expands the uniaxial deformation methods available, allowing to explore the mechanical, and strain-dependent physical properties of other anisotropic 2D materials more broadly.

Regulating the Electronic Structure of Bismuth Nanosheets by Titanium Doping to Boost CO2 Electroreduction and Zn-CO2 Batteries.

The electrochemical carbon dioxide reduction reaction (E-CO2 RR) to formate is a promising strategy for mitigating greenhouse gas emissions and addressing the global energy crisis. Developing low-cost and environmentally friendly electrocatalysts with high selectivity and industrial current densities for formate production is an ideal but challenging goal in the field of electrocatalysis. Herein, novel titanium-doped bismuth nanosheets (TiBi NSs) with enhanced E-CO2 RR performance are synthesized through one-step electrochemical reduction of bismuth titanate (Bi4 Ti3 O12 ). We comprehensively evaluated TiBi NSs using in situ Raman spectra, finite element method, and density functional theory. The results indicate that the ultrathin nanosheet structure of TiBi NSs can accelerate mass transfer, while the electron-rich properties can accelerate the production of *CO2 - and enhance the adsorption strength of *OCHO intermediate. The TiBi NSs deliver a high formate Faradaic efficiency (FEformate ) of 96.3% and a formate production rate of 4032 µmol h-1  cm-2 at -1.01 V versus RHE. An ultra-high current density of -338.3 mA cm-2 is achieved at -1.25 versus RHE, and simultaneously FEformate still reaches more than 90%. Furthermore, the rechargeable Zn-CO2 battery using TiBi NSs as a cathode catalyst achieves a maximum power density of 1.05 mW cm-2 and excellent charging/discharging stability of 27 h.

Decrypting the Electron-Withdrawing Effect of Au-Decorated Bi2 O3 for Efficient CO2 -to-Formate Electroreduction.

Although the electron-withdrawing effect of gold (Au) is highlighted in catalytic reactions, its enhancement mechanism for electron transport, especially in the electrochemical process, is still unclear. Herein, Au-decorated Bi2 O3 (Au-Bi2 O3 ) is proposed as a proof-of-concept to investigate the electron-withdrawing effect in the electrocatalytic CO2 reduction reaction (eCO2 RR) process. Evidence from in situ Raman spectra and in situ XRD tests reveals that, compared to Bi2 O3 , Bi species in Au-Bi2 O3 can be reduced to metallic Bi more rapidly and more easily driven by the electron-withdrawing effect of Au. The XPS tests after eCO2 RR further validates the transformation from Bi3+ to Bi0 in Au-Bi2 O3 is more complete. Meanwhile, in the in situ Fourier transform infrared (FTIR) spectra, the key intermediates (CO2 *- and OCHO*- ) appear at the more positive potential, indicating that metallic Bi is favorable for eCO2 RR due to the lower energy barrier as corroborated by density function theory (DFT) calculations. Au don't directly participate in the conversion from CO2 to formate as the reaction sites, but utilize the electron-withdrawing effect to motivate Bi-sites to deliver higher catalytic activity and higher selectivity to formate at a lower applied potential. This study not only has an insight into the electron-withdrawing effect of Au on the eCO2 RR process, but also develops a new perspective for engineering electron-withdrawing effect in electrocatalysts for high-efficient CO2 -to-formate conversion.

Orietation-controlled synthesis and Raman study of 2D SnTe.

Tin telluride (SnTe), as a narrow bandgap semiconductor material, has great potential for developing photodetectors with wide spectra and ultra-fast response. At the same time, it is also an important topological crystal insulator material, with different topological surface states on several common surfaces. Here, we introduce different Sn sources and control the growth of regular SnTe nanosheets along the (100) and (111) planes through the atmospheric pressure chemical vapor deposition method. It has been proven through various characterizations that the synthesized SnTe is a high-quality single crystal. In addition, the angular resolved Raman spectra of SnTe nanosheets grown on different crystal planes are first demonstrated. The experimental results showed that square SnTe nanosheets grown along the (100) plane exhibit in-plane anisotropy. At the same time, we use micro-nanofabrication technology to manufacture SnTe-based field effect transistors and photodetectors to explore their electrical and optoelectronic properties. It has been confirmed that transistors based on grown SnTe nanosheets exhibit p-type semiconductor characteristics and have a high response to infrared light. This work provides a new approach for the controllable synthesis of SnTe and adds new content to the research of SnTe-based infrared detectors.

Phytomediated-Assisted Preparation of Cerium Oxide Nanoparticles Using Plant Extracts and Assessment of Their Structural and Optical Properties.

Cerium oxide nanoparticles were obtained using aqueous extracts of Chelidonium majus and Viscum album. X-ray diffractometry analysis confirmed the crystalline structure of the synthesized cerium oxide nanoparticles calcined at 600 °C. Scanning electron microscopy, UV-Vis reflectance and Raman spectroscopy, XPS, and fluorescence studies were utilized to interpret the morphological and optical properties of these nanoparticles. The STEM images revealed the spherical shape of the nanoparticles and that they were predominantly uniform in size. The optical band gap of our cerium nanoparticles was determined to be 3.3 and 3.0 eV from reflectance measurements using the Tauc plots. The nanoparticle sizes evaluated from the Raman band at 464 cm-1 due to the F2g mode of the cubic fluorite structure of cerium oxide are close to those determined from the XRD and STEM data. The fluorescence results showed emission bands at 425, 446, 467, and 480 nm. The electronic absorption spectra have exhibited an absorption band around 325 nm. The antioxidant potential of the cerium oxide nanoparticles was estimated by DPPH scavenging assay.

Non-Invasive Detection of Biomolecular Abundance from Fermentative Microorganisms via Raman Spectra Combined with Target Extraction and Multimodel Fitting.

Biomolecular abundance detection of fermentation microorganisms is significant for the accurate regulation of fermentation, which is conducive to reducing fermentation costs and improving the yield of target products. However, the development of an accurate analytical method for the detection of biomolecular abundance still faces important challenges. Herein, we present a non-invasive biomolecular abundance detection method based on Raman spectra combined with target extraction and multimodel fitting. The high gain of the eXtreme Gradient Boosting (XGBoost) algorithm was used to extract the characteristic Raman peaks of metabolically active proteins and nucleic acids within E. coli and yeast. The test accuracy for different culture times and cell cycles of E. coli was 94.4% and 98.2%, respectively. Simultaneously, the Gaussian multi-peak fitting algorithm was exploited to calculate peak intensity from mixed peaks, which can improve the accuracy of biomolecular abundance calculations. The accuracy of Gaussian multi-peak fitting was above 0.9, and the results of the analysis of variance (ANOVA) measurements for the lag phase, log phase, and stationary phase of E. coli growth demonstrated highly significant levels, indicating that the intracellular biomolecular abundance detection was consistent with the classical cell growth law. These results suggest the great potential of the combination of microbial intracellular abundance, Raman spectra analysis, target extraction, and multimodel fitting as a method for microbial fermentation engineering.

Colossal 3D Electrical Anisotropy of MoAlB Single Crystal.

3D anisotropic functional properties (such as magnetic, electrical, thermal, and optical properties, etc.) in a single material are not only beneficial to the multipurpose of a material, but also helpful to enrich the regulatory dimensionality of functional materials. Herein, a colossal 3D electrical anisotropy of layered MAB-phase MoAlB single crystal is introduced and dissected. Using high-temperature metal-solution method, high-quality MoAlB single crystals are obtained and a surprisingly strong out-of-plane (σa /σb  = 1.43 × 105 , at 2 K) and in-plane (σa /σc  = 12.12, at 2 K) electrical anisotropies are first observed. After a series of experimental and theoretical investigations, it is demonstrated that the 3D anisotropic crystal structure and chemical bond of MoAlB result in its 3D anisotropic phonon vibration and electronic structure, influence the corresponding electron-electron as well as electron-phonon interactions, and finally give rise to its colossal 3D anisotropy of electrical conductivity. This work experimentally and theoretically proves MoAlB single crystal possessing the 3D anisotropies of crystal structure, chemical bond, phonon vibration, electronic structure, and electrical transport, but also provides a promising platform for the future design of functionalized electronic devices as well as synthesis of new and large-sized in-plane anisotropic 2D material (MoBene).

Construction, expression, purification, characterization, and structural analysis of microbial transglutaminase variants.

Microbial transglutaminase (MTG, EC 2.3.2.13) derived from Streptomyces mobaraensis is widely used in the food and pharmaceutical industry because of its ability to synthesize isopeptide bonds between the proteinogenic side chains of glutamine and lysine. The half-life (t1/2 ) of the activated wild-type enzyme at 60°C is 2 min. To improve the activity and thermostability of MTG for higher temperature application, three variants (Mut1, Mut2, and Mut3) were obtained by combining key amino acid mutations on the basis of previous research results. The best variant Mut2 with a specific combination of five of seven substitutions (S2P-S23V-Y24N-R215A-H289Y) shows a 10-fold increased half-life at 60°C (t1/2  = 27.6 min), and a 2.4-fold increased specific enzyme activity (39.3 U/mg). As measured by circular dichroism, the curve of Mut2 was basically the same as that of MTG-WT. The structural simulation of Mut2 shows that the overall structure is discoid with a crack, but the crack openings are wider than that of MTG-WT. Furthermore, structural analysis of Mut2 showed that there were seven hydrogen bonds and one π-anion interaction between Mut2 and its adjacent amino acids, and the number of hydrogen bonds was one more than that of MTG-WT (six hydrogen bonds).