Carbon nanotube electron blackbody and its radiation spectra.

An optical blackbody is an ideal absorber for all incident optical radiation, and the theoretical study of its radiation spectra paved the way for quantum mechanics (Planck's law). Herein, we propose the concept of an electron blackbody, which is a perfect electron absorber as well as an electron emitter with standard energy spectra at different temperatures. Vertically aligned carbon nanotube arrays are electron blackbodies with an electron absorption coefficient of 0.95 for incident energy ranging from 1 keV to 20 keV and standard electron emission spectra that fit well with the free electron gas model. Such a concept might also be generalized to blackbodies for extreme ultraviolet, X-ray, and γ-ray photons as well as neutrons, protons, and other elementary particles.

Machine learning of spectra-property relationship for imperfect and small chemistry data.

Machine learning (ML) is causing profound changes to chemical research through its powerful statistical and mathematical methodological capabilities. However, the nature of chemistry experiments often sets very high hurdles to collect high-quality data that are deficiency free, contradicting the need of ML to learn from big data. Even worse, the black-box nature of most ML methods requires more abundant data to ensure good transferability. Herein, we combine physics-based spectral descriptors with a symbolic regression method to establish interpretable spectra-property relationship. Using the machine-learned mathematical formulas, we have predicted the adsorption energy and charge transfer of the CO-adsorbed Cu-based MOF systems from their infrared and Raman spectra. The explicit prediction models are robust, allowing them to be transferrable to small and low-quality dataset containing partial errors. Surprisingly, they can be used to identify and clean error data, which are common data scenarios in real experiments. Such robust learning protocol will significantly enhance the applicability of machine-learned spectroscopy for chemical science.

Operando analysis reveals potential-driven in situ formation of single-Fe-atom electrocatalysts for green production of ammonia.

As a sustainable approach for N2 fixation, electrocatalytic N2 reduction reaction (N2RR) to produce ammonia (NH3) is highly desirable with a precise understanding to the structure-activity relationship of electrocatalysts. Here, firstly, we obtain a novel carbon-supported oxygen-coordinated single-Fe-atom catalyst for highly efficient production of ammonia from electrocatalytic N2RR. Based on such new type of N2RR electrocatalyst, by combining operando X-ray absorption spectra (XAS) with density function theory calculation, we reveal significantly that the as-prepared active coordination structure undergoes a potential-driven two-step restructuring, firstly from FeSAO4(OH)1a to FeSAO4(OH)1a'(OH)1b with the adsorption of another -OH on FeSA at open-circuit potential (OCP) of 0.58 VRHE, and subsequently restructuring from FeSAO4(OH)1a'(OH)1b to FeSAO3(OH)1a″ due to the breaking of one Fe-O bond and the dissociation of one -OH at working potentials for final electrocatalytic process of N2RR, thus revealing the first potential-induced in situ formation of the real electrocatalytic active sites to boost the conversion of N2 to NH3. Moreover, the key intermediate of Fe-NNHx was detected experimentally by both operando XAS and in situ attenuated total reflection-surface-enhanced infrared absorption spectra (ATR-SEIRAS), indicating the alternating mechanism followed by N2RR on such catalyst. The results indicate the necessity of considering the potential-induced restructuring of the active sites on all kinds of electrocatalysts for such as highly efficient ammonia production from N2RR. It also paves a new way for a precise understanding to the structure-activity relationship of a catalyst and helps the design of highly efficient catalysts.

Racial disparity in prostate cancer: an outlook in genetic and molecular landscape.

Prostate cancer (PCa) incidence, morbidity, and mortality rates are significantly impacted by racial disparities. Despite innovative therapeutic approaches and advancements in prevention, men of African American (AA) ancestry are at a higher risk of developing PCa and have a more aggressive and metastatic form of the disease at the time of initial PCa diagnosis than other races. Research on PCa has underlined the biological and molecular basis of racial disparity and emphasized the genetic aspect as the fundamental component of racial inequality. Furthermore, the lower enrollment rate, limited access to national-level cancer facilities, and deferred treatment of AA men and other minorities are hurdles in improving the outcomes of PCa patients. This review provides the most up-to-date information on various biological and molecular contributing factors, such as the single nucleotide polymorphisms (SNPs), mutational spectrum, altered chromosomal loci, differential gene expression, transcriptome analysis, epigenetic factors, tumor microenvironment (TME), and immune modulation of PCa racial disparities. This review also highlights future research avenues to explore the underlying biological factors contributing to PCa disparities, particularly in men of African ancestry.

Strongly Bound Excitons and Anisotropic Linear Absorption in Monolayer Graphullerene.

Graphullerene is a novel two-dimensional carbon allotrope with unique optoelectronic properties. Despite significant experimental characterization and prior density functional theory calculations, unanswered questions remain as to the nature, energy, and intensity of the electronic and optical excitations. Here, we present first-principles calculations of the quasiparticle band structure, neutral excitations, and absorption spectra of monolayer graphullerene and bulk graphullerite, employing the GW-Bethe-Salpeter equation (GW-BSE) approach. We show that strongly bound excitons dominate the absorption spectrum of monolayer graphullerene with binding energies up to 0.8 eV, while graphullerite exhibits less pronounced excitonic effects. Our calculations also reveal a strong linear polarization anisotropy, reflecting the in-plane structural anisotropy from intermolecular coupling between neighboring C60 units. We further show that the presence of Mg atoms, crucial to the synthesis process, induces structural modifications and polarizability effects, resulting in a ∼1 eV quasiparticle gap renormalization and a reduction in the exciton binding energy to ∼0.6 eV.

Chromatograms and Mass Spectra of High-Mannose and Paucimannose N-Glycans for Rapid Isomeric Identifications.

N-Linked glycosylation is one of the most essential post-translational modifications of proteins. However, N-glycan structural determination remains challenging because of the small differences in structures between isomers. In this study, we constructed a database containing collision-induced dissociation MSn mass spectra and chromatograms of high-performance liquid chromatography for the rapid identification of high-mannose and paucimannose N-glycan isomers. These N-glycans include isomers by breaking of arbitrary numbers of glycosidic bonds at arbitrary positions of canonical Man9GlcNAc2 N-glycans. In addition, some GlcMannGlcNAc2 N-glycan isomers were included in the database. This database is particularly useful for the identification of the N-glycans not in conventional N-glycan standards. This study demonstrated the application of the database to structural assignment for high-mannose N-glycans extracted from bovine whey proteins, soybean proteins, human mammary epithelial cells, and human breast carcinoma cells. We found many N-glycans that are not expected to be generated by conventional biosynthetic pathways of multicellular eukaryotes.

Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states.

PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH+) in the wildtype (WT) PcyA-BV complex, and a nearby catalytic residue Asp105 was found to have two conformations (protonated and deprotonated). Semiempirical calculations have suggested that the protonation states of BV are reflected in the absorption spectrum of the WT PcyA-BV complex. In the previously determined absorption spectra of the PcyA D105N and I86D mutants, complexed with BV, a peak at 730 nm, observed in the WT, disappeared and increased, respectively. Here, we performed neutron crystallography and quantum chemical analysis of the D105N-BV and I86D-BV complexes to determine the protonation states of BV and the surrounding residues and study the correlation between the absorption spectra and protonation states around BV. Neutron structures elucidated that BV in the D105N mutant is in a neutral state, whereas that in the I86D mutant is dominantly in a protonated state. Glu76 and His88 showed different hydrogen bonding with surrounding residues compared with WT PcyA, further explaining why D105N and I86D have much lower activities for phycocyanobilin synthesis than the WT PcyA. Our quantum mechanics/molecular mechanics calculations of the absorption spectra showed that the spectral change in D105N arises from Glu76 deprotonation, consistent with the neutron structure. Collectively, our findings reveal more mechanistic details of bilin pigment biosynthesis.

Isotopically non-stationary 13 C metabolic flux analysis of two closely related fast-growing cyanobacteria, Synechococcus elongatus PCC 11801 and 11802.

Synechococcus elongatus PCC 11801 and 11802 are closely related cyanobacterial strains that are fast-growing and tolerant to high light and temperature. These strains hold significant promise as chassis for photosynthetic production of chemicals from carbon dioxide. A detailed quantitative understanding of the central carbon pathways would be a reference for future metabolic engineering studies with these strains. We conducted isotopic non-stationary 13 C metabolic flux analysis to quantitively assess the metabolic potential of these two strains. This study highlights key similarities and differences in the central carbon flux distribution between these and other model/non-model strains. The two strains demonstrated a higher Calvin-Benson-Bassham (CBB) cycle flux coupled with negligible flux through the oxidative pentose phosphate pathway and the photorespiratory pathway and lower anaplerosis fluxes under photoautotrophic conditions. Interestingly, PCC 11802 shows the highest CBB cycle and pyruvate kinase flux values among those reported in cyanobacteria. The unique tricarboxylic acid (TCA) cycle diversion in PCC 11801 makes it ideal for the large-scale production of TCA cycle-derived chemicals. Additionally, dynamic labeling transients were measured for intermediates of amino acid, nucleotide, and nucleotide sugar metabolism. Overall, this study provides the first detailed metabolic flux maps of S. elongatus PCC 11801 and 11802, which may aid metabolic engineering efforts in these strains.

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.

Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.

BACKGROUND: Studying the composition rules and evolution mechanisms of genome sequences are core issues in the post-genomic era, and k-mer spectrum analysis of genome sequences is an effective means to solve this problem. RESULT: We divided total 8-mers of genome sequences into 16 kinds of XY-type due to XY dinucleotides number in 8-mers. Previous works explored that the independent unimodal distributions observed only in three CG-type 8-mer spectra, while non-CG type 8-mer spectra have not the universal phenomenon from prokaryotes to eukaryotes. On this basis, we analyzed the distribution variation of non-CG type 8-mer spectra across 889 animal genome sequences. Following the evolutionary order of animals from primitive to more complex, we found that the spectrum distributions gradually transition from unimodal to tri-modal. The relative distance from the average frequency of each non-CG type 8-mers to the center frequency is different within a species and among different species. For the 8-mers contain CG dinucleotides, we further divided these into 16 subsets, where each 8-mer contains both CG and XY dinucleotides, called XY1_CG1 subsets. We found that the separability values of XY1_CG1 spectra are closely related to the evolution and specificity of animals. Considering the constraint of Chargaff's second parity rule, we finally obtained 10 separability values as the feature set to characterize the evolution state of genome sequences. In order to verify the rationality of the feature set, we used 14 common classification algorithms to perform binary classification tests. The results showed that the accuracy (Acc) ranged between 98.70% and 83.88% among birds, other vertebrates and mammals. CONCLUSION: We proposed a credible feature set to characterizes the evolution state of genomes and obtained satisfied results by the feature set on large scale classification of animals.

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.

The role of microenvironments on computed vibrationally-resolved emission spectra: The case of oxazines.

Oxazine dyes act as reporters of their near environment by the response of their fluorescence spectra. At the same time, their fluorescence spectra exhibit a pronounced vibrational progression. In this work, we computationally investigate the impact of near-environment models consisting of aggregated water as well as betaine molecules on the vibrational profile of fluorescence spectra of different oxazine derivatives. For aggregated betaine and a water molecule located above the plane of the dyes, we observe a distinct modification of the vibrational profile, which is more pronounced than the effect of a continuum description of a solvent environment. Our analysis shows that this effect cannot be explained by a pure change in the electronic structure, but that also vibrational degrees of freedom of the environment can be decisive for the vibrational profile and should, hence, not generally be neglected.

Ab initio multireference calculation of electronic spectra of the osmium complexes, [Os(bpy) 3 ] 2 + and [Os(phen) 3 ] 2 + .

The spin-orbit coupling corrected absorption spectra of osmium complexes, [Os(bpy) 3 ] 2 + and [Os(phen) 3 ] 2 + , were calculated by using ab initio multireference perturbation method (NEVPT2) with relativistic effects taken into account throughout ZORA approximation and corresponding all-electron basis sets. For the same purpose, the time-dependent DFT techniques were used. A very good agreement between NEVPT2 and experimental spectra should be highlighted, especially for the MLCT transitions that occur in visible and near-UV regions ( 16 , 000 - 33 , 000 cm - 1 ). Moreover, the present study offers description of excited states of titled osmium complexes and their spectra interpretation using molecular orbitals.

Structure and intermolecular interactions in ionic liquid 1-ethyl-3-methylimidazolium bromide and its aqueous solutions investigated by vibrational spectroscopy and quantum chemical computations.

The recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions (S. A. Katsyuba, S. Spicher, T. P. Gerasimova, S. Grimme, J. Phys. Chem. B 2020, 124, 6664) is applied to ionic liquid (IL) 1-ethyl-3-methylimidazolium bromide (EmimBr), its C2-deuterated analog [Emim-d]Br and its aqueous solutions. It is shown that the solvation strongly modifies frequencies and IR intensities of the CH/CD stretching vibrations (νCH/νCD) of the imidazolium ring. The main vibrational spectroscopic features of the neat IL are reproduced by the simulations for a cluster (EmimBr)9, in which all three imidazolium CH moieties of the solvated cation form short contacts with three Br- anions, and another two Br- anions are located on top and bottom of imidazolium ring. Cluster models of aqueous solutions reproduce the experimental vibrational frequencies of actual solutions, provided that the Br- anion of solvated contact ion pair (CIP) is situated on top of imidazolium ring, and CH/CD moieties of the latter participate in short contacts with surrounding water molecules. Both structural and spectroscopic analysis allow to interpret the short contacts CH/CD⋯Br- and CH/CD⋯OH2 as hydrogen bonds of approximately equal strength. Enthalpies of bonding of these liquid-state H-bonds, estimated with the use of empirical correlations, amount to ca. 1.4 kcal⋅mol-1, while the analogous estimates obtained for the gas-phase charged species [Emim]2Br+ increase to 5.6 kcal⋅mol-1. It is shown that formation of solvent-shared ion pair (SIP) in aqueous solution, where the counterions of IL are separated by two water molecules H-bonded to a Br- anion, produces frequency shifts ΔνCH/CD, strongly different from the case of CIP formation. This difference can be used for IR/Raman spectroscopic differentiation of the type of solvated ion pairs of EmimBr or other related ILs.

Aromatic and magnetic properties in a series of heavy rare earth-doped Ge6 cluster anions.

A series of pentagonal bipyramidal anionic germanium clusters doped with heavy rare earth elements, REGe 6 - (RE = Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu), have been identified at the PBE0/def2-TZVP level using density functional theory (DFT). Our findings reveal that the centrally doped pentagonal ring structure demonstrates enhanced stability and heightened aromaticity due to its uniform bonding characteristics and a larger charge transfer region. Through natural population analysis and spin density diagrams, we observed a monotonic decrease in the magnetic moment from Gd to Yb. This is attributed to the decreasing number of unpaired electrons in the 4f orbitals of the heavy rare earth atoms. Interestingly, the system doped with Er atoms showed lower stability and anti-aromaticity, likely due to the involvement of the 4f orbitals in bonding. Conversely, the systems doped with Gd and Tb atoms stood out for their high magnetism and stability, making them potential building blocks for rare earth-doped semiconductor materials.

Quantum mechanical study of transition metal hydrides: Comparison of determined molecular properties with experimental data.

This study compares results of four relativistic pseudopotential basis sets, which differ mainly by their size: double-zeta introduced by Hay and Wadt from Los Alamos National Laboratory (LANL2DZ), triple-zeta based on Stuttgart energy-consistent scalar-relativistic pseudopotential (SDD3), its extension with 2fg polarization functions, and combination of Stuttgart pseudopotentials with quintuple-zeta cc-pV5Z base (SDD5). Hydrides of transition metals from Cr to Zn group are chosen as reference molecules. The coupled cluster method (CCSD(T)) is used for evaluation of selected molecular characteristics. Interatomic distances, dissociation energies, vibration modes, and anharmonicity constants are determined and compared with available experimental data. As expected, the accuracy of basis depends mainly on its size. However, only moderate modification of SDD3 basis set significantly improves its accuracy, which becomes comparable to the largest basis set. Nevertheless, the time consumption is significantly lower.

Quantum cluster equilibrium theory applied to liquid ammonia.

Through this paper, the authors propose using the quantum cluster equilibrium (QCE) theory to reinvestigate ammonia clusters in the liquid phase. The ammonia clusters from size monomer to hexadecamer were considered to simulate the liquid ammonia in this approach. The clusterset used to model the liquid ammonia is an ensemble of different structures of ammonia clusters. After studious research of the representative configurations of ammonia clusters through the cluster research program ABCluster, the configurations have been optimized at the MN15/6-31++G(d,p) level of theory. These optimizations lead to geometries and frequencies as inputs for the Peacemaker code. The QCE study of this molecular system permits us to get the liquid phase populations in a temperature range of 190-260 K, covering the temperatures from the melting point to the boiling point. The results show that the population of liquid ammonia comprises mainly the ammonia hexadecamer followed by pentadecamer, tetradecamer, and tridecamer. We noted that the small-sized ammonia clusters do not contribute to the population of liquid ammonia. In addition, the thermodynamic properties, such as heat of vaporization, heat capacity, entropy, enthalpy, and free energies, obtained by the QCE theory have been compared to the experiment given some relatively good agreements in the gas phase and show considerable discrepancies in liquid phase except the density. Finally, based on the predicted population, we calculated the infrared spectrum of liquid ammonia at 215 K temperature. It comes out that the calculated infrared spectrum qualitatively agrees with the experiment.

Ab initio electronic absorption spectra of para-nitroaniline in different solvents: Intramolecular charge transfer effects.

Intramolecular charge transfer (ICT) effects of para-nitroaniline (pNA) in eight solvents (cyclohexane, toluene, acetic acid, dichloroethane, acetone, acetonitrile, dimethylsulfoxide, and water) are investigated extensively. The second-order algebraic diagrammatic construction, ADC(2), ab initio wave function is employed with the COSMO implicit and discrete multiscale solvation methods. We found a decreasing amine group torsion angle with increased solvent polarity and a linear correlation between the polarity and ADC(2) transition energies. The first absorption band involves π → π* transitions with ICT from the amine and the benzene ring to the nitro group, increased by 4%-11% for different solvation models of water compared to the vacuum. A second band of pNA is characterized for the first time. This band is primarily a local excitation on the nitro group, including some ICT from the amine group to the benzene ring that decreases with the solvent polarity. For cyclohexane, the COSMO implicit solvent model shows the best agreement with the experiment, while the explicit model has the best agreement for water.

Facile and Green Synthesis of Well-Defined Nanocrystal Oxygen Evolution Catalysts by Rational Crystallization Regulation.

The development of catalysts for an economical and efficient oxygen evolution reaction (OER) is critical for clean and sustainable energy storage and conversion. Nickel-iron-based (NiFe) nanostructures are widely investigated as active OER catalysts and especially shape-controlled nanocrystals exhibit optimized surface structure and electronic properties. However, the structural control from amorphous to well-defined crystals is usually time-consuming and requires multiple stages. Here, a universal two-step precipitation-hydrothermal approach is reported to prepare a series of NiFe-based nanocrystals (e.g., hydroxides, sulfides, and molybdates) from amorphous precipitates. Their morphology and evolution of atomic and electronic structure during this process are studied using conclusive microscopy and spectroscopy techniques. The short-term, additive-free, and low-cost method allows for the control of the crystallinity of the materials and facilitates the generation of nanosheets, nanorods, or nano-octahedra with excellent water oxidation activity. The NiFe-based crystalline catalysts exhibit slightly compromised initial activity but more robust long-term stability than their amorphous counterparts during electrochemical operation. This facile, reliable, and universal synthesis method is promising in strategies for fabricating NiFe-based nanostructures as efficient and economically valuable OER electrocatalysts.

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.