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Here, we have designed an efficient N 2 reduction reaction (NRR) catalyst with diatomic Pd-Cu sites on N-doped porous carbon by modifying single-atom Pd sites with Cu. The catalyst achieves high Faradaic efficiency and a desirable yield rate for NH 3 electrosynthesis under ambient conditions, outperforming the individual single-atom counterparts.
The nitrogenase superfamily constitutes a large and diverse ensemble of two–component metalloenzymes. These systems couple the hydrolysis of ATP to the reduction of disparate substrates from diatomic gases (Mo and alternative nitrogenases) to photosynthetic pigments (protochlorophyllide and chlorophyllide oxidoreductases). Only very recently have the activities of the highly divergent and paraphyletic Group IV nitrogenases begun to be uncovered. In conclusion, this review highlights the first characterized member of this group, which was found to catalyze an unprecedented reaction in the coenzyme F430 biosynthetic pathway, and the catalytic potential of a superfamily that has yet to be fully explored.
Abstract Despite its sizable errors, density functional theory (DFT) is extensively used to evaluate thermochemical properties of gases, liquids and their interfaces with solids. As numerous halogen‐containing compounds appear as reactants, products and/or electrolytes in electrochemical reactions, and ionic effects are currently an active area of research, it is important to evaluate the accuracy of DFT for halogen thermochemistry. Herein, we assess the formation energies of interhalogens, hydrogen halides, diatomic and atomic halogens and their ions using six widespread functionals at the GGA, meta‐GGA and hybrid levels. We observe that DFT errors with respect to experiments are correlated with the electronegativity of the species and there are systematic trends across functionals, such that swift corrections were devised. Specifically, the average of the mean absolute errors for the six functionals decreased from 0.19 eV before the corrections to 0.08 eV after them. Besides, the overall maximum absolute error (MAX) decreased from 0.76 to 0.44 eV and the average of the MAXs decreased from 0.51 to 0.24 eV. Finally, we illustrate the qualitative and quantitative impact of gas‐phase errors on the predictions of surface Pourbaix diagrams.
Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, in this study, the performance of two different ab initio composite approaches for obtaining equilibrium structures, “energy scheme” and “geometry scheme,” is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.
Quantifying phytoplankton composition is critical to predicting marine ecosystem structure and function. DNA meta-barcoding and high-performance liquid chromatography (HPLC) pigment analysis are two widely used methods for assessing phytoplankton composition; however, comparing their performance has been done only rarely. Here, we integrate DNA meta-barcoding and HPLC pigment observations to determine eukaryotic phytoplankton composition in the Santa Barbara Channel, California. We find that both methods identify the same four dominant eukaryotic phytoplankton taxa (diatoms, dinoflagellates, chlorophytes, and prymnesiophytes), but inter- and intra-lineage variability in biomarker pigmentation (associated with both a lack of taxonomic specificity of biomarker pigments and intrinsic differences in accessory pigmentation) drives substantial disagreement between the methods. Covariation network analysis circumvents this disagreement and reveals that diverse assemblages of phytoplankton and other protists covary with distinct suites of biomarker pigments. Our results highlight the strengths and weaknesses of each method in characterizing phytoplankton composition and reveal novel insights into phytoplankton physiology that could only be gained by integrating the two methods. Finally, we suggest a path to monitor eukaryotic plankton communities on unprecedented spatiotemporal scales based on the covariation of unique phytoplankton and protistan assemblages with remotely sensible phytoplankton pigment concentrations.
Abstract Nano‐ and picophytoplankton are a major component of open‐ocean ecosystems and one of the main plankton functional types in biogeochemical models, yet little is known about their trace metal contents. In cultures of the picoeukaryote Ostreococcus lucimarinus , iron limitation reduced iron quotas by 68%, a fraction of the plasticity known in diatoms. In contrast, a commonly co‐occurring cyanobacterium, Prochlorococcus , showed variable iron contents with iron availability in culture. Synchrotron X‐ray fluorescence was used to measure single‐cell metal (Mn, Fe, Co, Ni, Zn) quotas of autotrophic flagellates (1.4–16.8‐ μ m diameter) collected from four ocean regions. Iron quotas were tightly constrained and showed little response to iron availability, similar to cultured Ostreococcus . Zinc quotas also did not vary with zinc availability but appeared to vary with phosphorus availability. These results suggest that macronutrient and metal availability may be equally important for controlling metal contents of small eukaryotic open‐ocean phytoplankton.
Abstract Fluvial silicon (Si) plays a critical role in controlling primary production, water quality, and carbon sequestration through supporting freshwater and marine diatom communities. Geological, biogeochemical, and hydrological processes, as well as climate and land use, dictate the amount of Si exported by streams. Understanding Si regimes—the seasonal patterns of Si concentrations—can help identify processes driving Si export. We analyzed Si concentrations from over 200 stream sites across the Northern Hemisphere to establish distinct Si regimes and evaluated how often sites moved among regimes over their period of record. We observed five distinct regimes across diverse stream sites, with nearly 60% of sites exhibiting multiple regime types over time. Our results indicate greater spatial and interannual variability in Si seasonality than previously recognized and highlight the need to characterize the watershed and climate variables that affect Si cycling across diverse ecosystems.
A direct optical absorption diagnostic has been developed for rotationally resolved measurements of diatomic carbon (a 3 Π u →d 3 Π g (0,0) and (1,1)) at a repetition rate of 525 kHz and resolution of 7.3 pm over the range of 511.1–514.1 nm. The diagnostic utilizes a high-power pulsed continuum laser light source dispersed in a spectrograph and imaged by a high-speed camera. Measurements have been performed that capture the temporal evolution of C 2 number density and temperature of a cloud of carbon black sublimating in shock heated gas at high temperature and pressure (T = 5500 K, P = 3.7 atm). A simultaneous light absorption measurement of the condensed phase enables comparisons of the gaseous C 2 number density to the condensed phase mass. The continuum laser absorption diagnostic is applied to C 2 in this work but shows promise in being a simple “drop-in” system for absorption spectroscopy in the visible range at rapid repetition rates and high dispersion, filling an important gap for laser diagnostic systems.
One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. Here, this process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn 4 CaO 5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn 4 CaO 5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S 0 → S 1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).
Dissociative recombination (DR) reactions are important when modeling charged species in the presence of free electrons. While experimental measurements of DR reaction rates are challenging, surface hopping ab initio molecular dynamics (SH-AIMD) simulations provide an attractive alternative. SH-AIMD is especially well-suited for estimating branching ratios, i.e., the relative rates of competing production channels, for DR reactions. Although the radiolysis of diatomic tritium has been studied experimentally, previous attempts to model these systems have failed to account for isotope effects in DR reactions. Previous SH-AIMD studies have also not investigated tritium isotope effects for the branching ratios of DR reactions. In this study, we compute the DR branching ratios of the protiated and tritiated ketenyl ion. Comparison with literature values for the protiated branching ratios provides confidence in the reliability of our SH-AIMD results. Our simulations predict a significant increase of the HC + CO branching ratio for the tritiated system.
In this work, we present SpectrumSDT – a program for calculations of energies and lifetimes of bound rotational-vibrational states below and scattering resonances above the dissociation threshold on a global potential energy surface of a triatomic system, which may include stable molecules, weekly-bound van-der-Waals complexes, and unbound atom + diatom scattering systems. Large-amplitude vibrational motion is treated explicitly using hyper-spherical coordinates. Three options for the rotational-vibrational interaction are supported: uncoupled (symmetric top rotor), partially coupled (to include interaction between several nearest states only) and full-coupled (vibrating asymmetric-top rotor). In addition to energies and lifetimes, SpectrumSDT is able to integrate ro-vibrational wave functions over the user-defined regions of potential energy surface, which helps to classify these states. In this release of the code, SpectrumSDT is limited to ABA-type molecules with wave functions that do not extend into the regions near Eckart singularities.
We report that studies related to U gas-phase oxidation through plasma- and thermo-chemistry are important for many fields, including environmental monitoring, forensic analysis, debris analysis in a weapon detonation event, and nucleation physics. Recently, significant efforts have been made to understand the chemical pathways involved in the progression from U atoms to diatoms (UO) and polyatomic molecules (UxOy), employing optical spectroscopy tools and computational modeling. In many studies, laser ablation of U or a U-containing flow reactor are used as a highly resource-efficient, repeatable, tunable, and lab-scale testbed for studying gas-phase oxidation in U plasmas. The spectroscopic analysis of high-temperature gas-phase oxidation of U is challenging due to the congested U spectra, resolution limitations of instrumentation, and the numerous chemical reaction pathways possible. This article focuses on the current understanding and challenges related to studying U plasma chemistry, specifically U gas-phase oxidation and molecular formation, via optical spectroscopy of plasmas and associated computational and spectral modeling. The physical and chemical processes involved in the evolution from U atoms to U oxide molecules to nanoparticles and agglomerates (i.e., debris) are discussed in the context of optical spectroscopic studies. The article concludes by highlighting opportunities for future research efforts based on existing knowledge published in the literature.
Medium-chain fatty acids (e.g., C8-C14) are important biofuel precursors that can be produced from CO2 by cyanobacteria and other photoautotrophs. However, cyanobacteria naturally direct a relatively small fraction of fixed carbon to lipid synthesis, primarily producing long-chain membrane-bound fatty acids. We investigated whether mitigating kinetic bottlenecks within the fatty acid biosynthesis (FAB) pathway could enhance flux to free fatty acid (FFA) production in Picosynechococcus sp. PCC 7002. Previous in vitro studies proposed that the FAB initiating enzyme FabH is the primary rate-controlling enzyme in PCC 7002. We hypothesized that enhancing fatty acid initiation could increase in vivo FFA production while shifting the kinetic bottleneck further downstream in the pathway. We enabled C8-FFA accumulation by knocking out the native acyl-acyl carrier protein synthetase gene (aas) and expressing the highly active Cuphea palustris-derived mutant thioesterase CpFatB1.2-M4-287 (CupTE), which selectively catalyzes C8 chain termination. We then expressed the diatom-derived Chaetoceros sp. GSL56 FabH ortholog (chKASIII), to enhance initiation, and a medium-chain selective E. coli ketosynthase ecFabF[I108F] (ecFabF∗), to enhance elongation. When expressed individually or in combination with ecFabF∗, chKASIII slowed growth and decreased net carbon fixation rates relative to the parental Δaas-CupTE strain. However, co-expression of chKASIII, ecFabF∗, and CupTE redirected a larger fraction of fixed carbon toward FFA production, increasing relative carbon flux to C8-FFA and decreasing the projected minimum selling price by four-fold. This work demonstrates how systems metabolic engineering can be applied to enhance C8-FFA production in cyanobacteria while highlighting the unpredictable physiological consequences of host metabolic burden.
The chemistry evolution in a laser ablation plume depends strongly on its initial physical conditions. In this article, we investigate the impact of plasma generation conditions on the interrelated phenomena of expansion dynamics, plasma chemistry, and physical conditions. Plasmas are produced from a uranium metal target in air using nanosecond, femtosecond, and femtosecond filament-assisted laser ablation. Time-resolved two-dimensional spectral imaging was performed for evaluating the spatio-temporal evolu-tion of atoms, diatoms, polyatomic molecules, and nanoparticles in situ. Emission spectral features reveal that molecular formation occurs at early times in both femtosecond and filament ablation plumes, although with different temporal decay. In contrast, mo-lecular formation is found to occur at much later times in nanosecond plasma evolution. Spectral modeling is used to infer tem-poral behavior of plasma excitation temperature, and results highlighted that nanosecond plume temperatures decay rapidly while plumes generated by filament ablation show slowest decay. In this work, we find U atoms and UO molecules co-exist in ultrafast laser produced plasmas even at early times after plasma onset owing to favorable temperatures for molecular formation. Regardless of irradiation conditions, plume emission features showed presence of higher oxides (i.e. UxOy), although with different temporal histories. Our study provides insight into the impact of plasma generation conditions on chemistry evolution in plasmas produced from traditional focused femtosecond, nanosecond, and filament-assisted laser ablation.
Mixtures of gas-phase hydrogen isotopologues (diatomic combinations of protium, deuterium, and tritium) can be separated using columns containing a solid such as palladium that reversibly absorbs hydrogen. A temperature-swing process can transport hydrogen into or out of a column by inducing temperature-dependent absorption or desorption reactions. Here, we consider two designs: a thermal cycling absorption process, which moves hydrogen back and forth between two columns, and a simulated moving bed (SMB), where columns are in a circular arrangement. We present a numerical mass and heat transport model of absorption columns for hydrogen isotope separation. It includes a detailed treatment of the absorption–desorption reaction for palladium. By comparing the isotope concentrations within the columns as a function of position and time, we observe that SMB can lead to sharper separations for a given number of thermal cycles by avoiding the remixing of isotopes.
To uncover the way Hartree–Fock exchange brings static correlation error into hybrid Kohn–Sham density functional theory, we compare the potential energy curves of four diatomic molecules, namely, H 2 , F 2 , HF, and NaF, using both restricted and unrestricted Kohn–Sham theory. Here, we find that increasing the percentage of Hartree–Fock exchange significantly increases the static correlation error because Hartree–Fock exchange replaces the ability of local exchange in density functionals to account for the localization effects associated with static correlation.
While CCSD(T) with spin-restricted Hartree-Fock (RHF) orbitals has long been lauded for its ability to accurately describe closed-shell interactions, the performance of CCSD(T) on open-shell species is much more erratic, especially when using a spin-unrestricted HF (UHF) reference. Previous studies have shown improved treatment of open-shell systems when a non-HF set of molecular orbitals, like Brueckner or Kohn-Sham density functional theory (DFT) orbitals, is used as a reference. Inspired by the success of regularized orbital-optimized second-order Møller-Plesset perturbation theory (κ-OOMP2) orbitals as reference orbitals for MP3, we investigate the use of κ-OOMP2 orbitals and various DFT orbitals as reference orbitals for CCSD(T) calculations of the corrected ground-state harmonic vibrational frequencies of a set of 36 closed-shell (29 neutrals, 6 cations, 1 anion) and 59 open-shell diatomic species (38 neutrals, 15 cations, 6 anions). The aug-cc-pwCVTZ basis set is used for all calculations. The use of κ-OOMP2 orbitals in this context alleviates difficult cases observed for both UHF orbitals and OOMP2 orbitals. Removing two multireference systems and 12 systems with ambiguous experimental data leaves a pruned data set. Overall performance on the pruned data set highlights CCSD(T) with a B97 orbital reference (CCSD(T):B97), CCSD(T) with a κ-OOMP2 orbital reference (CCSD(T):κ-OOMP2), and CCSD(T) with a B97M-rV orbital reference (CCSD(T):B97M-rV) with RMSDs of 8.48 cm -1 , and 8.50 cm -1 , and 8.75 cm -1 respectively, outperforming CCSD(T):UHF by nearly a factor of 5. Moreover, the performance on the closed- and open-shell subsets shows these methods are able to treat open-shell and closed-shell systems with comparable accuracy and robustness. CCSD(T) with RHF orbitals is seen to improve upon UHF for the closed-shell species, while spatial symmetry breaking in a number of restricted open-shell HF (ROHF) references leads CCSD(T) with ROHF reference orbitals to exhibit the poorest statistical performance of all methods surveyed for open-shell species. The use of κ-OOMP2 orbitals has also proven useful in diagnosing multireference character that can hinder the reliability of CCSD(T).
The dipole moment is the molecular property that most directly indicates molecular polarity. The accuracy of computed dipole moments depends strongly on the quality of the calculated electron density, and the breakdown of single-reference methods for strongly correlated systems can lead to poor predictions of the dipole moments in those cases. Here, we derive the analytical expression for obtaining the electric dipole moment by multiconfiguration pair density functional theory (MCPDFT), and we assess the accuracy of MC-PDFT for predicting dipole moments at equilibrium and nonequilibrium geometries. We show that MC-PDFT dipole moment curves have reasonable behavior even for stretched geometries, and they significantly improve upon the CASSCF results by capturing more electron correlation. Herein, the analysis of a dataset consisting of 18 first-row transition metal diatomics and 6 main-group polyatomic molecules with multireference character suggests that MC-PDFT and its hybrid extension (HMC-PDFT) perform comparably to CASPT2 and MRCISD+Q methods and have a mean unsigned deviation of 0.2–0.3 D with respect to the best available dipole moment reference values. We explored the dependence of the predicted dipole moments upon the choice of the on-top density functional and active space, and we recommend the tPBE and hybrid tPBE0 on-top choices for the functionals combined with the moderate correlated participating orbital scheme for selecting the active space. With these choices, the mean unsigned deviations (in debyes) of the calculated equilibrium dipole moments from the best estimates are 0.77 for CASSCF, 0.29 for MC-PDFT, 0.24 for HMCPDFT, 0.28 for CASPT2, and 0.25 for MRCISD+Q. These results are encouraging because the computational cost of MC-PDFT or HMC-PDFT is largely reduced compared to the CASPT2 and MRCISD+Q methods.