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Organic phosphate compound synthesis, purification and use in detection of enzymatic activity in soils by fluorescence after biological oxidation
With environmental regulations limiting the use of volatile organic compounds, low-vapor pressure solvents have replaced traditional degreasing solvents for bond substrate preparation. When used to clean and prepare porous bond substrates such as phenolic composites, low vapor pressure solvents can penetrate deep into substrate pore networks and remain there for extended periods. Trapped solvents can interact with applied adhesives either prior to or during cure, potentially compromising bond properties. Currently, methods for characterizing solvent time-depth profiles in bond substrates are limited to bulk gravimetric or sectioning techniques. While sectioning techniques such as microtome allow construction of solvent depth profiles, their depth resolution and reliability are limited by substrate type. Sectioning techniques are particularly limited near the adhesive-substrate interface where depth resolution is further limited by adhesive-substrate hardness and, in the case of a partially cured adhesive, mechanical properties differences. Additionally, sectioning techniques cannot provide information about lateral solvent diffusion. Cross-section component mapping is an alternative method for measuring solvent migration in porous substrates that eliminates the issues associated with sectioning techniques. With cross-section mapping, the solvent-wiped substrate is sectioned perpendicular rather than parallel to the wiped surface, and the sectioned surface is analyzed for the solvent or solvent components of interest using a two-dimensional mapping or imaging technique. Solvent mapping can be performed using either direct or indirect methods. With a direct method, one or more solvent components are mapped using red or Raman spectroscopy together with a moveable sample stage and/or focal plane array detector. With an indirect method, an elemental "tag" not present in the substrate is added to the solvent before the substrate is wiped. Following cross sectioning, the tag element can then be mapped by its characteristic x-ray emission using either x-ray fluorescence, or electron-beam energy-and wavelength-dispersive x-ray spectrometry. The direct mapping techniques avoid issues of different diffusion or migration rates of solvents and elemental tags, while the indirect techniques avoid spectral resolution issues in cases where solvents and substrates have adjacent or overlapping peaks. In this study, cross-section component indirect mapping is being evaluated as a method for measuring migration of d-limonene based solvents in glass-cloth phenolic composite (GCP) prior to and during subsequent bonding and epoxy adhesive cure.
An open‐source modeling platform, called Anaerobic Digestion Model No. 1 Fast (ADM1F), is introduced to achieve fast and numerically stable simulations of anaerobic digestion processes. ADM1F is compatible with an iPython interface to facilitate model configuration, simulation, data analysis, and visualization. Faster simulations and more stable results are accomplished by implementing an advanced open‐source library of numerical methods called Portable Extensive Toolkit for Scientific Computation (PETSc) to solve the ADM1 system of equations. Leveraging PETSc, ADM1F can consistently complete a steady‐state simulation under 0.2 s, over 99% faster than a benchmark ADM1 model implemented with MATLAB while achieving agreement of model outputs within 1% of those obtained with the benchmark model. For dynamic simulations, however, ADM1F has a computational speed advantage only when the influent characteristics update more frequently than every 4 h. The ability of ADM1F to be useful as a tool to study anaerobic digestion systems is demonstrated through two example implementations of ADM1F: (1) a two‐phase co‐digestion scenario evaluating the impact of the organic loading rate and the substrate composition on reactor performance and stability, and (2) a conventional digester scenario assessing the effectiveness of recovery strategies after disruptions that led to instability. These examples demonstrate how the high simulation speed and the convenience of the iPython interface allow ADM1F to complete complex analyses within minutes, much faster than computational strategies currently reported in the literature.
The expanding toolbox of functionalization chemistries for selectively installing moieties on specific sites of a substrate underpins almost all modern organic and biochemical syntheses. Likewise, the installation of mobile guest ions in specific interstitial sites and their transport along specific diffusion pathways forms the basis of modern lithium (Li)-ion battery electrodes. Many insertion hosts afford a diverse range of accessible interstitial sites. However, site-selective positioning of cations with atomic precision remains almost entirely unexplored. Here, we show that by deciphering site preferences of co/pre-intercalated cations, we can position Li ions in four distinct sites within a 1D ζ-V 2 O 5 insertion host. The use of topochemistry to effect single-crystal-to-single-crystal transformations enables atomic-resolution mapping of the selective positioning of Li ions through single-crystal X-ray diffraction. Here we image interstitial sites that are occupied at high depths of discharge, thereby obtaining unprecedented structural insight into “fully stuffed” frameworks critical for the realization of high-energy-density intercalation electrodes.
Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNA UTu1 , a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNA UTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.
Thin films of elemental metals play a very important role in modern electronic nano-devices as conduction pathways, spacer layers, spin-current generators/detectors, and many other important functionalities. In this work, by exploiting the chemistry of solid metal-organic source precursors, we demonstrate the molecular beam epitaxy synthesis of elemental Ir and Ru metal thin films. The synthesis of these metals is enabled by thermodynamic and kinetic selection of the metal phase as the metal-organic precursor decomposes on the substrate surface. Film growth under different conditions was studied using a combination of in situ and ex situ structural and compositional characterization techniques. The critical role of substrate temperature, oxygen reactivity, and precursor flux in tuning film composition and quality is discussed in the context of precursor adsorption, decomposition, and crystal growth. Computed thermodynamics quantifies the driving force for metal or oxide formation as a function of synthesis conditions and changes in chemical potential. These results indicate that bulk thermodynamics are a plausible origin for the formation of Ir metal at low temperatures, while Ru metal formation is likely mediated by kinetics.
The demand for energy has increased significantly to meet the development of the economy and the increasing population. With the continuous consumption of energy, the shortage of non-renewable resources and the greenhouse effect have aroused worldwide attention. Therefore, the conversion of one-carbon substrates such as formate, methanol, and carbon dioxide (CO 2 ) as sustainable feedstocks into high-value-added products is a potential way to address such concerns. Although one-carbon substrates can be converted into organics by natural pathways, these pathways may not be optimal due to the multiple enzymes involved and remarkable amounts of energy consumption. Thus, synthetic biology, as an emerging field, offers a new approach to boost one-carbon bioconversion.
Glass film less than five mils thick is formed from powdered glass dispersed in an organic liquid, deposited on a substrate, and fused into place. The thin films can be cut and shaped for contact lenses, optical filters and insulating layers.
The results of three experimental studies related to the inorganic/organic battery separator operating mechanism are described: saponification of the plasticizer, resistivity of the simulated separators, and zincate diffusion through the separators. The inorganic/organic separator appears to be a particular example of a general class of ionic conducting films composed of inorganic fillers and/or substrates bonded together by an organic polymer containing an incompatible plasticizer that may be leached by the electrolyte. The I/O separator functions as a microporous film of varying tortuosity with essentially no specific chemical inhibition to zincate diffusion.
For the most part, enzymes contain one active site wherein they catalyze in a serial manner chemical reactions between substrates both efficiently and rapidly. Imagine if a situation could be created within a chiral porous crystal containing trillions of active sites where substrates can reside in vast numbers before being converted in parallel into products. Here, we report how it is possible to incorporate 1-anthracenecarboxylate (1-AC – ) as a substrate into a γ-cyclodextrin-containing metal–organic framework (CD-MOF-1), where the metals are K + cations, prior to carrying out [4+4] photodimerizations between pairs of substrate molecules, affording selectively one of four possible regioisomers. One of the high-yielding regioisomers exhibits optical activity as a result of the presence of an 8:1 ratio of the two enantiomers following separation by high-performance liquid chromatography. The solid-state superstructure of 1-anthracenecarboxylate potassium salt (1-ACK), which is co-crystallized with γ-cyclodextrin, reveals that pairs of substrate molecules are not only packed inside tunnels between spherical cavities present in CD-MOF-1, but also stabilized—in addition to hydrogen-bonding to the C-2 and C-3 hydroxyl groups on the d-glucopyranosyl residues present in the γ-cyclodextrin tori—by combinations of hydrophobic and electrostatic interactions between the carboxyl groups in 1-AC– and four K + cations on the waistline between the two γ-cyclodextrin tori in the tunnels. Here, these non-covalent bonding interactions result in preferred co-conformations that account for the highly regio- and enantioselective [4+4] cycloaddition during photoirradiation. Theoretical calculations, in conjunction with crystallography, support the regio- and stereochemical outcome of the photodimerization.
Microporous two-dimensional covalent organic framework (2D COF) membranes offer promise for gas separation applications, but their gas transport mechanism remains unclear. In this study, a TpHz 2D COF membrane supported on a macroporous nylon substrate is prepared by substrate-assisted interfacial polymerization under mild conditions. The formation of a continuous and dense thin (~300 nm thick) TpHz layer is confirmed by scanning electron microscopy and Fourier transform infrared spectroscopy. Characterization by X-ray diffraction, grazing incidence wide-angle X-ray scattering, and N 2 porosimetry qualitatively reveals the microstructures of the supported TpHz membranes, i.e., they comprise partially oriented 2D COF lamellar crystallites with moderate crystallinity in an eclipsed (AA) stacking geometry, centering the effective membrane pore size distribution at ~1.1 nm. Further, single gas permeation data show that the transport of common molecular gases, including H 2 , He, CH 4 , N 2 , and CO 2 , through the synthesized TpHz membranes follows the Knudsen transport mechanism, where single gas permeance decreases with an increasing molecular weight and permeation temperature. Binary gas separation results show that in the equimolar CO 2 /N 2 mixture, the presence of the CO 2 surface flow slightly hinders the N 2 flow at room temperature due to the reduced membrane channel size by the adsorbed CO 2 gas layer on TpHz’s pore wall. In contrast, permeation of the equimolar CH 4 /N 2 binary mixture does not exhibit a discernible surface flow of both gases due to their much lower gas uptake on TpHz, and their transport mechanism follows Knudsen-like behavior.
A long excited state lifetime is a desirable quality of photocatalysts because it enables a higher probability of energy or electron transfer from the photocatalyst to a substrate. Yet, achieving a long lifetime in organic (metal-free) catalysts is challenged by competing rapid nonradiative relaxation from excited states and relatively slow intersystem crossing into long-lived states with different spin multiplicity. Here, we propose an intersystem crossing mechanism in heavy-metal free photocatalyst that results from reorganization of a dihedral angle between moieties. The relaxation of orthogonality of the dihedral angle and increasing the orbital overlap between the two components of the molecule changes the coupling between the configurations of singlet and triplet states, which in turn results in larger spin orbit coupling between the two manifolds as the molecule twists. We predict that this enables intersystem crossing to outcompete the singlet state lifetime.
An account is given of the thermal performance and ablation characteristics of the NASA-Ames Lightweight Ceramic Ablators (LCAs) in supersonic, high-enthalpy convective environments, which use low density ceramic or carbon fiber matrices as substrates for main structural support, with organic resin fillers. LCA densities are in the 0.224-1.282 g/cu cm range. In-depth temperature data have been obtained to determine thermal penetration depths and conductivity. The addition of SiC and PPMA is noted to significantly improve the ablation performance of LCAs with silica substrates. Carbon-based LCAs are the most mass-efficient at high flux levels.
The metabolic action of selected fungi species on common components of the interior of Space Station Freedom (SSF) will be tested. When present, volatile organic chemicals will be collected on porous polymer adsorbent columns. Using thermal desorption, the volatile compounds will be passed onto a gas chromatographic column for analysis. The Space Station Freedom (SSF) modular complex will largely be individually self contained and the established air environment will not be easily adjusted. The development and maintenance of a safe working environment offers a considerable challenge. Present plans for use of SSF acknowledge periods of manned activities and alternate times when the station is unmanned. The obvious necessity for clean and safe air and water during periods of use have been pursued as fundamental systems to SSF success. Somewhat less obvious, although perhaps of no less importance to the success of long term cyclic usage, are those periods of inactivity. It is during these periods when spores from microorganisms may be afforded the best conditions to germinate and in the vegetative form react with the complex synthetic chemical polymers which compose the furnishings and hardware of SSF nodes. Biodegradation could constitute a real hygiene problem, if the organisms form and release volatile organic chemicals. Similar problems have been documented in closed and improperly ventilated buildings and work spaces. Many of the metabolic products of fungi and bacterial growth create a variety of health problems. Analytical chemical techniques will first be used to document the growth of Aspergillus, Penicillium, and Cladosporium fungal species on the potential substrates Nomex and Kevlar. Any volatile organics that are released will be measured using the spectrum of gas adsorption chromatography. The level of microbial contamination that is necessary to produce such volatile compounds and the relative amounts expected to accumulate will be estimated.
The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction half-life at 50 C, and to reveal the effect of functional groups on reactivity. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable (i. e. acetate decarboxylation half-life was l0(exp 18) years at 50 C); whereas, organic substances containing two oxygenated groups in which one group was a beta-positioned carbonyl group were the most reactive (i. e. acetoacetate decarboxylation half-life was l0(exp-2) years at 50 C). Of all functional groups the beta-positioned carbonyl group (aldehyde or ketone) was the strongest activating group, giving rates of reaction that were up to 10(exp 24)-times faster than rates of similar molecules lacking the beta-carbonyl group. From this knowledge of organic reactivity and the inherent constraints of autocatalytic processes, we concluded that an origins-of-life process based on autocatalytic transformation of C,H,O-substrates was constrained to using the most reactive organic molecules that contain alpha- or beta-carbonyl groups, since small autocatalytic domains of plausible catalytic power that used less reactive substrates could not carry out chemical transformations fast enough to prevent catastrophic efflux (escape) of reaction intermediates. Knowledge of the kinetics of organic transformations is useful, not only in constraining the chemistry of the earliest autocatalytic process related to the origin of life, but also in establishing the relative reactivity of organic molecules on the early Earth and other planets that may or may not be related to the origin of life.
Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function. Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of 13C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that mycorrhizal-driven differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater micro8ial diversity than ectomycorrhizal (ECM) soils. When incubated with 13C enriched substrates, substrate type drove shifts in the identity of active decomposers and their metabolic products in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and specialized function. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.
The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA Pyl ) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA Pyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA Pyl and reveal the emergence of tRNA Pyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA Pyl species with the more common G73-containing tRNA Pyl will enable future efforts to engineer PylRS systems for further genetic code expansion.
This paper presents a novel sol-gel method to synthesize large and thick silica aerogel monoliths at near ambient conditions using a commercial aqueous solution of colloidal silica nanoparticles as building blocks. To achieve slabs with high visible transmittance and low thermal conductivity, the method combines the strategies of (i) synthesizing gels on an omniphobic perfluorocarbon liquid substrate, (ii) aging at temperatures above room temperature, and (iii) performing solvent exchange with a low-surface-tension organic solvent prior to ambient drying. The omniphobic liquid substrates were used to prevent cracking and ensure an optically-smooth surface, while nanoparticle building blocks were small (<10 nm) to limit volumetric light scattering. Gels were aged at temperatures between 25 and 80 °C for up to 21 days to make them stronger and stiffer and to reduce shrinkage and cracking during ambient drying. Ambient drying was achieved by first exchanging water in the gel pores for octane, followed by drying in an octane-rich atmosphere to decrease capillary forces. The synthesized nanoparticle-based silica aerogel monoliths had thicknesses up to 5 mm, diameters up to 10 cm, porosities exceeding 80%, and thermal conductivities as low as 0.08 W m –1 K –1 . Notably, the slabs featured visible transmittance exceeding 75% even for slabs as thick as 5 mm. The as-synthesized aerogel monoliths were exposed to TMCS vapor to induce hydrophobic properties resulting in a water contact angle of 140° that prevented water infiltration into the pores and protected the aerogels from water damage. This simple synthesis route conducted at near ambient conditions produces hydrophobic aerogel monoliths with promising optically transparent and thermally insulating properties that can be adhered to glass panes for window insulation and solar-thermal energy conversion applications.