A new semiconductor heterojunction SERS substrate for ultra-sensitive detection of antibiotic residues in egg.

Antibiotic residues in animal-derived food (egg) are threatening human health. Semiconductor heterojunction surface-enhanced Raman scattering (SERS) substrates can be used for ultra-sensitive detection of antibiotic residues in egg. Here, a TiO2/ZnO heterojunction was developed as a new SERS substrate based on an interface engineering strategy. Due to strong interfacial coupling and efficient carrier separating in heterostructure, utilization rate of photo-induced electrons in substrate was improved greatly, which realized the efficient charge transfer in substrate-molecule system, resulting in a prominent SERS enhancement. Taking the detection of enrofloxacin residue in egg as an example, the limit of detection (LOD) is only 13.1 µg/kg, which is far below the European Union standard, and lower than LODs of other conventional analytical methods and existing noble metal-based SERS methods. More importantly, benefiting from high sensitivity and selectivity of heterojunction and fingerprint characteristics of SERS, multiple antibiotic residues in egg can be identified simultaneously.

One-pot synthesis of nano Zr-based metal-organic frameworks for fluorescence determination of quercetin and Hg2.

In this study, a nanoscale Zr-based metal-organic framework (nano-Zr-MOF) was prepared by one-pot method using meso-tetra(4-carboxyphenyl)porphyrin as organic ligand and Zr4+ as metal unit. The nanoscale structure endows it with excellent dispersion in water. The nano-Zr-MOF exhibited intense red fluorescence, which could be significantly quenched by the addition of quercetin, probably due to its electron-rich framework. The high selectivity for quercetin detection was verified with analogues and common ions as interfering agents. Moreover, the nano-Zr-MOF could be used as a highly selective and sensitive sensor for the detection of Hg2+. The detection limits for quercetin and Hg2+ were 0.026 µM and 0.039 µM, respectively. This fluorometric method was successfully applied to detect quercetin in red wine and food samples with satisfactory recoveries ranging from 83.7-112.3% and 81.8-115.9%, respectively. The recovery in detection of Hg2+ in lake water were ranging from 97.1-109.2%.

Molecular Structure of Gaseous Oxopivalate Co(II): Electronic States of Various Multiplicities.

Synchronous electron diffraction/mass spectrometry was used to study the composition and structure of molecular forms existing in a saturated vapor of cobalt(II) oxopivalate at T = 410 K. It was found that monomeric complexes Co4O(piv)6 dominate in the vapor. The complex geometry possesses the C3 symmetry with bond lengths Co-Oc = 1.975(5) Å and Co-O = 1.963(5) Å, as well as bond angles Oc-Co-O = 111.8(3)°, Co-Oc-Co = 110.4(6)°, O-Co-O = 107.1(3)° in the central OcCo4 fragment and four OcCoO3 fragments. The presence of an open 3d shell for each Co atom leads to the possibility of the existence of electronic states of the Co4O(piv)6 complex with Multiplicities 1, 3, 5, 7, 9, 11, and 13. For them, the CASSCF and XMCQDPT2 calculations predict similar energies, identical shapes of active orbitals, and geometric parameters, the difference between which is comparable with the error of determination by the electron diffraction experiment. QTAIM and NBO analysis show that the Co-Oc and Co-O bonds can be attributed to ionic (or coordination) bonds with a significant contribution of the covalent component. The high volatility and simple vapor composition make it possible to recommend cobalt (II) oxopivalate as precursors in the preparation of oxide films or coatings in the CVD technologies. The features of the electronic and geometric structure of the Co4O(piv)6 complex allows for the conclude that only a very small change in energy is required for the transition from antiferromagnetically to ferromagnetically coupled Co atoms.

Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms.

Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D models that are often reliable for substantial parts of the macromolecules. However, the extent of rotational searches in particle detection has not been investigated due to computational limitations. Here, we provide a GPU implementation of TM as part of the PyTOM software package, which drastically speeds up the orientational search and allows for sampling beyond the Crowther criterion within a feasible timeframe. We quantify the improvements in sensitivity and false-discovery rate for the examples of ribosome identification and detection. Sampling at the Crowther criterion, which was effectively impossible with CPU implementations due to the extensive computation times, allows for automated extraction with high sensitivity. Consequently, we also show that an extensive angular sample renders 3D TM sensitive to the local alignment of tilt series and damage induced by focused ion beam milling. With this new release of PyTOM, we focused on integration with other software packages that support more refined subtomogram-averaging workflows. The automated classification of ribosomes by TM with appropriate angular sampling on locally corrected tomograms has a sufficiently low false-discovery rate, allowing for it to be directly used for high-resolution averaging and adequate sensitivity to reveal polysome organization.

Defect-poor BaSn(OH)6 enhanced charge separation for efficient photocatalytic degradation of toluene.

Crystal defect is well-known to have a significant effect on the photocatalytic performance of semiconductors. Herein, defect-rich and -poor BaSn(OH)6 (BSOH-Sn and BSOH-Ba) photocatalysts were synthesized by exchanging the addition order of Ba and Sn. Results show that the defect-poor BSOH-Ba exhibited more efficient toluene degradation under ultraviolet (UV) light, which could attribute to the great suppression of photogenerated electron-hole (e--h+) pairs recombination by tuning the defect concentration. The low defect concentration in BSOH-Ba finally promotes the charge separation efficiency, the generation of reactive oxygen species (ROS), and the photocatalytic toluene degradation reactions. This work not only provides an effective way to inhibit the recombination of photogenerated carriers and improve the photocatalytic performance, but also promotes the understanding of defective perovskite-type hydroxide for more photoreactions.

Structure and function relationship of formate dehydrogenases: an overview of recent progress.

Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.

Electron Donor-Acceptor (EDA) Complex between a Triarylamine and B(C6F5)3 for the Photocatalytic Dehydrogenative Cross-Coupling of Phenols.

In this article, an electron donor-acceptor (EDA) complex between a triarylamine and B(C6F5)3 that catalyzes the dehydrogenative cross-coupling of phenols is described. We demonstrate, for the first time, that the use of both components of the radical ion pairs generated by the photoexcitation of the EDA complex as co-catalysts, and the triarylaminium radical cation (+·NAr3) successfully promotes dehydrogenative cross-coupling between electron-rich phenols and 2-naphthols to provide electron-rich biphenol motifs using molecular oxygen as a terminal oxidant.

Ballistic Brownian Motion of Nanoconfined DNA.

Theoretical treatments of polymer dynamics in liquid generally start with the basic assumption that motion at the smallest scale is heavily overdamped; therefore, inertia can be neglected. We report on the Brownian motion of tethered DNA under nanoconfinement, which was analyzed by molecular dynamics simulation and nanoelectrochemistry-based single-electron shuttle experiments. Our results show a transition into the ballistic Brownian motion regime for short DNA in sub-5 nm gaps, with quality coefficients as high as 2 for double-stranded DNA, an effect mainly attributed to a drastic increase in stiffness. The possibility for DNA to enter the underdamped regime could have profound implications on our understanding of the energetics of biomolecular engines such as the replication machinery, which operates in nanocavities that are a few nanometers wide.

Fragmentation of the DNA Lesion 8-oxo-Guanine by Low-Energy Electrons.

8-oxo-Guanine is a mutagenic lesion produced by reactions involving reactive oxygen species and guanine in DNA. Its production induces mispairing between the canonical nucleobases during DNA replication such that various types of cancers are associated with the DNA lesion. Since radiation therapy is used in some cases, the interaction of low-energy electrons with 8-oxo-guanine can in turn produce other reactive species, which in principle could have either a detrimental or protective effect on the organism. Motivated by these facts, we report a comparative experimental study of electron-induced fragmentation of guanine and 8-oxo-guanine, along with a theoretical study of the π* shape resonances and bound anion states, which may trigger those dissociation reactions. The electron-induced fragmentation of 8-oxo-guanine is remarkably distinct from the native form. More complex reactions were observed for the oxidized species, which may produce several anion fragments at very low energies (∼0 eV). The dehydrogenated parent anion, which is already a minor fragment in guanine, was completely suppressed in 8-oxo-guanine. The calculated thermodynamical thresholds also suggest that NH2 elimination in guanine, at sub-excitation energies, proceeds via a complex reaction involving rearrangement steps.

High pressure freezing and cryo-sectioning can be used for protein structure determination by electron diffraction.

Electron diffraction of three-dimensional nanometer sized crystals has emerged since 2013 as an efficient technique to solve the structure of both small organic molecules and model proteins. However, the major bottleneck of the technique when applied to protein samples is to produce nano-crystals that do not exceed 200 to 300 nm in at least one dimension and to deposit them on a grid while keeping the minimum amount of solvent around them. Since the presence of amorphous solvent around the crystal, necessary to preserve its integrity, increases the amount of diffuse scattering, thus degrading the signal-to noise ratio of the diffraction signal, other sample preparation strategies have been developed. One of them is the milling of thin crystal lamella using focused ion beam (FIB), which was successfully applied to several protein crystals. Here, we present a new approach that uses cryo-sectioning after high pressure freezing of dextran embedded protein crystals. 150 to 200 nm thick cryo-sections of hen egg white lysozyme tetragonal crystals where used for electron diffraction experiments. Complete diffraction data up to 2.9 Å resolution have been collected and the lysozyme structure has been solved by molecular replacement and refined against these data. Our data demonstrate that cryo-sectioning can preserve protein structure at high resolution and can be used as a new sample preparation technique for 3D electron diffraction experiments of protein crystals. The different orientations found in the crystal chips and their large number resulting from the cryo-sectioning make the latter an attractive approach as it combines advantages from both blotting approaches (number of crystals) and FIB-milling (controlled thickness and absence of solvent around the crystal).

A Chimeric NiFe Hydrogenase Heterodimer to Assess the Role of the Electron Transfer Chain in Tuning the Enzyme's Catalytic Bias and Oxygen Tolerance.

The observation that some homologous enzymes have the same active site but very different catalytic properties demonstrates the importance of long-range effects in enzyme catalysis, but these effects are often difficult to rationalize. The NiFe hydrogenases 1 and 2 (Hyd 1 and Hyd 2) from E. coli both consist of a large catalytic subunit that embeds the same dinuclear active site and a small electron-transfer subunit with a chain of three FeS clusters. Hyd 1 is mostly active in H2 oxidation and resistant to inhibitors, whereas Hyd 2 also catalyzes H2 production and is strongly inhibited by O2 and CO. Based on structural and site-directed mutagenesis data, it is currently believed that the catalytic bias and tolerance to O2 of Hyd 1 are defined by the distal and proximal FeS clusters, respectively. To test these hypotheses, we produced and characterized a hybrid enzyme made of the catalytic subunit of Hyd 1 and the electron transfer subunit of Hyd 2. We conclude that catalytic bias and sensitivity to CO are set by the catalytic subunit rather than by the electron transfer chain. We confirm the importance of the proximal cluster in making the enzyme Hyd 1 resist long-term exposure to O2, but we show that other structural determinants, in both subunits, contribute to O2 tolerance. A similar strategy based on the design of chimeric heterodimers could be used in the future to elucidate various structure-function relationships in hydrogenases and other multimeric metalloenzymes and to engineer useful hydrogenases that combine the desirable properties of distinct, homologous enzymes.

Dissociation process of polyalanine aggregates by free electron laser irradiation.

Polyalanine (polyA) disease-causative proteins with an expansion of alanine repeats can be aggregated. Although curative treatments for polyA diseases have not been explored, the dissociation of polyA aggregates likely reduces the cytotoxicity of polyA. Mid-infrared free electron laser (FEL) successfully dissociated multiple aggregates. However, whether the FEL dissociates polyA aggregates like other aggregates has not been tested. Here, we show that FEL at 6.1 µm experimentally weakened the extent of aggregation of a peptide with 13 alanine repeats (13A), and the irradiated 13A exerted lesser cytotoxicity to neuron-like cells than non-irradiated 13A. Then, we applied molecular dynamics (MD) simulation to follow the dissociation process by FEL. We successfully observed how the intermolecular ß-sheet of polyA aggregates was dissociated and separated into monomers with helix structures upon FEL irradiation. After the dissociation by FEL, water molecules inhibited the reformation of polyA aggregates. We recently verified the same dissociation process using FEL-treated amyloid-ß aggregates. Thus, a common mechanism underlies the dissociation of different protein aggregates that cause different diseases, polyA disease and Alzheimer's disease. However, MD simulation indicated that polyA aggregates are less easily dissociated than amyloid-ß aggregates and require longer laser irradiation due to hydrophobic alanine repeats.

Electron Transfer Beyond the Outer Membrane: Putting Electrons to Rest.

Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond-an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.

Distance-Regulated Photoelectrochemical Sensor "Signal-On" and "Signal-Off" Transitions for the Multiplexed Detection of Viruses Exposed in the Aquatic Environment.

Photochemical (PEC) sensors were severely limited for multiplex detection applications due to the cross interference between multiplex signals at the single recognition interface. In this work, a distance-regulated PEC sensor was developed for multiplex detection by using an i-Motif sequence with conformational transformation activity as the signal transduction unit. Through dynamic regulation of the spatial distance between the end site of the functional sequence and the electrode material, the photogenerated electrons on the surface of the sensor were directionally transferred. Thus, a PEC sensor with "signal-on" and "signal-off" dual signal output modes was developed for simultaneous detection of multitarget molecules. Combining isothermal nucleic acid amplification, the PEC sensor constructed in this work was successfully applied to the detection of two virus (Norovirus and Rotavirus) nucleic acid sequences. Under the optimal condition, this bioassay protocol exhibits a linear range of 0.01-100 nM for both viruses with detection limits of 0.72 and 0.53 pM, respectively. In this study, a stimulus-mediated distance regulation strategy successfully addressed the transduction of multiplex detection signals at the single recognition interface of the PEC sensor. It is expected that the technical barriers to multiplex detection of PEC sensors will be overcome and the application of PEC sensing technology will be expanded in the field of environmental analysis.

Interpreting pH-Dependent Differential UV/VIS Absorbance Spectra to Characterize Carboxylic and Phenolic Chromophores in Natural Organic Matter.

Natural organic matter (NOM) is critical for the biogeochemical cycles of energy and many elements in terrestrial and aquatic ecosystems, and protonation-active functional groups in NOM molecules, notably carboxylic and phenolic groups often mediate these critical environmental functions. Molecular heterogeneity, polydispersity and dynamic behavior of NOM complicate achieving an unambiguous description of its molecular properties and reactivity. This study demonstrates that differential ultraviolet-visible (UV/VIS) absorbance spectra (DAS) of NOM acquired at varying pH values exhibit several distinct features associated with the deprotonation of NOM molecules, independent of the environmental provenance of NOM (e.g., surface water, seawater, sediment, and wastewater). The protonation-active functionalities that contribute to the Gaussian distribution bands present in the DAS were identified here by comparing characteristic properties of the bands with the stoichiometries of NOM molecules ascertained by Ultrahigh-Resolution Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS). The protonation-active individual chromophores universally present in NOM molecules were identified by a genetic molecular network analysis. The observed DAS features were closely modeled via superimposing DAS spectra of 51 individual protonation-active chromophores. Molecular orbital theory was applied to further interpret the deprotonation of these chromophores, their molecular structure, electron distribution, and electron transitions measured using DAS. The high sensitivity and easy implementation of the DAS approach allows using it as a powerful tool to quantify the molecular properties and reactivity of NOM at environmental concentrations.

A DFT study of ethanol interaction with the bimetallic clusters of PtSn and its implications on reactivity.

The comprehension of the factors affecting the adsorption of ethanol over metals and metal alloys is a crucial step for the rational development of new catalysts for hydrogen production through ethanol reforming. In this work, we analyze the effect of combining Pt and Sn on a metal cluster on the complexation energy and reactivity for OH dehydrogenation of ethanol. Metal clusters of Pt10, Sn10 and Pt5Sn5 had their putative minimum located with the help of the artificial bee colony algorithm. Whereas the isolated Pt cluster shows a high degree of polarization (ESP surface), the Sn cluster shows a quite uniform electron density surface. The PtSn cluster is strongly polarized, with Pt atoms withdrawing electron density of Sn atoms. Complexation occurs with the oxygen atom of ethanol directed towards the point of highest electron potential in the ESP surface. Pt presents the highest complexation energy, -20.90 kcal/mol, against only -7.83 kcal/mol (at the B97-3c level). For the PtSn cluster, the value is intermediate, namely -12.39 kcal/mol. The more malleable electron density of Pt and its electron affinity are responsible for its highest complexation energy. These characteristics are partially transferred to the PtSn cluster. QTAIM results show that, for the PtSn cluster, the O-H bond in ethanol is somewhat weaker than for pure Pt and Sn. As a consequence, the energy barrier for the O-H dehydrogenation has its lowest value for the PtSn cluster, which shows that the alloying of two metals can lead to quite quite unexpected results opening the perspective for a more rational fine tuning of catalysts properties.

Theoretical investigation of novel electron donors for bulk heterojunction solar cells with potential photovoltaic characteristics.

Engineering electronic organic donor materials are one of the most critical steps in producing bulk-heterojunction solar cells (BHJ) with good photovoltaic properties. Compared to standard donor materials, electron donors derived from thiophene have made significant progress as they can be better suited for optoelectronics and are cheaper and more stable. Therefore, the use of new thiophene derivatives (M1-M4) as donor molecules in BHJs has been the subject of this extensive theoretical analysis. Density functional theory (DFT) and time-dependent DFT (TD-DFT) computations have been used to investigate the boundary molecular orbital (FMO) analysis, the density of states analysis, electron and hole reorganization energy, molecular electrostatic potential, global reactivity parameters, and photovoltaic properties. The effects of end-donor modifications on the photovoltaic and electronic characteristics of the new molecules (M1-M4) are investigated. According to the results, the molecules have good optical properties, a small band gap, a perfect open-circuit voltage, and a good alignment energy level between the designated donor molecules and the acceptor phenyl-C61-butyric acid methyl ester (PCBM). These results suggest that further research in this area could enhance the efficacy of organic solar cells.

Pulse parameter optimizer: an efficient tool for achieving prescribed dose and dose rate with electron FLASH platforms.

Purpose. Commercial electron FLASH platforms deliver ultra-high dose rate doses at discrete combinations of pulse parameters including pulse width (PW), pulse repetition frequency (PRF) and number of pulses (N), which dictate unique combinations of dose and dose rates. Additionally, collimation, source to surface distance, and airgaps also vary the dose per pulse (DPP). Currently, obtaining pulse parameters for the desired dose and dose rate is a cumbersome manual process involving creating, updating, and looking up values in large spreadsheets for every treatment configuration. This work presents a pulse parameter optimizer application to match intended dose and dose rate precisely and efficiently.Methods. Dose and dose rate calculation methods have been described for a commercial electron FLASH platform. A constrained optimization for the dose and dose rate cost function was modelled as a mixed integer problem in MATLAB (The MathWorks Inc., Version9.13.0 R2022b, Natick, Massachusetts). The beam and machine data required for the application were acquired using GafChromic film and alternating current current transformers (ACCTs). Variables for optimization included DPP for every collimator, PW and PRF measured using ACCT and airgap factors.Results. Using PW, PRF,Nand airgap factors as parameters, a software was created to optimize dose and dose rate, reaching the closest match if exact dose and dose rates are not achievable. Optimization took 20 s or less to converge to results. This software was validated for accuracy of dose calculation and precision in matching prescribed dose and dose rate.Conclusion. A pulse parameter optimization application was built for a commercial electron FLASH platform to increase efficiency in dose, dose rate, and pulse parameter prescription process. Automating this process reduces safety concerns associated with manual look up and calculation of these parameters, especially when many subjects at different doses and dose rates are to be safely managed.

Molecular architecture and electron transfer pathway of the Stn family transhydrogenase.

The challenge of endergonic reduction of NADP+ using NADH is overcome by ferredoxin-dependent transhydrogenases that employ electron bifurcation for electron carrier adjustments in the ancient Wood-Ljungdahl pathway. Recently, an electron-bifurcating transhydrogenase with subunit compositions distinct from the well-characterized Nfn-type transhydrogenase was described: the Stn complex. Here, we present the single-particle cryo-EM structure of the Stn family transhydrogenase from the acetogenic bacterium Sporomusa ovata and functionally dissect its electron transfer pathway. Stn forms a tetramer consisting of functional heterotrimeric StnABC complexes. Our findings demonstrate that the StnAB subunits assume the structural and functional role of a bifurcating module, homologous to the HydBC core of the electron-bifurcating HydABC complex. Moreover, StnC contains a NuoG-like domain and a GltD-like NADPH binding domain that resembles the NfnB subunit of the NfnAB complex. However, in contrast to NfnB, StnC lost the ability to bifurcate electrons. Structural comparison allows us to describe how the same fold on one hand evolved bifurcation activity on its own while on the other hand combined with an associated bifurcating module, exemplifying modular evolution in anaerobic metabolism to produce activities critical for survival at the thermodynamic limit of life.

Accelerated electron and mass transfer through constructing H2WO4/Ti3C2/g-C3N4 Z-scheme photocatalyst for environmental remediation.

The catalytic efficiency of photocatalysts highly depends on electron transport and mass transfer. Herein, we designed and prepared an effective H2WO4/Ti3C2/g-C3N4 (HTC) Z-scheme heterojunction through interfacial engineering strategy. The results manifested that 97.4% of Cr(VI) (80 µM, 50 mL) could be removed by HTC heterojunction within 10 min under visible light irradiation. The reduction rate constant of Cr(VI) for H2WO4/g-C3N4 (HC) heterojunction increased by a factor of 21 after introducing the conductive Ti3C2. Moreover, 96% of tetracycline (TC, 10 mg L-1, 50 mL) could be degraded by HTC heterojunction within 30 min. The electronic conductivity and ionic diffusion coefficient of HC heterojunction increased by a factor of 64 and 1064 after adding Ti3C2, respectively. This result indicated that the introduction of highly conductive Ti3C2 significantly improved the electron and mass transfer of the heterojunction. Meanwhile, the HCT heterojunction displayed favorable photocurrent, and keep excellent photostability during the long-term test. Moreover, density functional theory (DFT) calculations demonstrated that the internal electric field (IEF) from g-C3N4 to H2WO4 in HCT heterojunction promotes the combination of the photoinduced electrons in the H2WO4 conduction band (CB) with photoinduced holes in the g-C3N4 valence band (VB), thus accelerating the charge transfer in the HCT Z-scheme heterojunction. The antibacterial efficiency of HTC heterojunction against E. coli and S. aureus could reach up to 98.4% and 99.7%, respectively. The degradation intermediates and the potential degradation mechanism of TC were analyzed and proposed based on the results of HPLC-MS analysis. Moreover, the toxicity of TC and degradation intermediates were estimated by Toxicity Estimation Software (T.E.S.T.) based on quantitative structure-activity relationship (QSAR). This work provided a valuable guideline for designing the effective MXene-based Z-scheme heterojunction for environmental remediation.