Chemiresistive Detection of Gaseous Hydrocarbons and Interrogation of Charge Transport in Cu[Ni(2,3-pyrazinedithiolate)[subscript 2]] by Gas Adsorption
Abstract not provided
Aubrey, Michael L.↗
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Results for “CIS”
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The pineapple genome and the evolution of CAM photosynthesis
Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C 3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Lastly, we found pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C 3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.
59 BASIC BIOLOGICAL SCIENCES↗
A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs
The spike (S) protein of SARS-CoV-2 is delivered to the virion assembly site in the ER-Golgi Intermediate Compartment (ERGIC) from both the ER and cis-Golgi in infected cells. However, the relevance and modulatory mechanism of this bidirectional trafficking are unclear. Here, using structure-function analyses, we show that S incorporation into virus-like particles (VLP) and VLP fusogenicity are determined by coatomer-dependent S delivery from the cis-Golgi and restricted by S-coatomer dissociation. Although S mimicry of the host coatomer-binding dibasic motif ensures retrograde trafficking to the ERGIC, avoidance of the host-like C-terminal acidic residue is critical for S-coatomer dissociation and therefore incorporation into virions or export for cell-cell fusion. Because this C-terminal residue is the key determinant of SARS-CoV-2 assembly and fusogenicity, our work provides a framework for the export of S protein encoded in genetic vaccines for surface display and immune activation.
60 APPLIED LIFE SCIENCES↗
Catalytic carbon–carbon bond cleavage in lignin via manganese–zirconium-mediated autoxidation
Abstract Efforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl–ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon–carbon (C–C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C–C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to cis,cis -muconic acid in an engineered strain of Pseudomonas putida KT2440 that conducts aromatic O -demethylation reactions at the 4-position. This work demonstrates that autoxidation of lignin with Mn and Zr offers a catalytic strategy to increase the yield of valuable aromatic monomers from lignin.
09 BIOMASS FUELS↗
Visualization of clustered protocadherin neuronal self-recognition complexes
Neurite self-recognition and avoidance are fundamental properties of all nervous systems. These processes facilitate dendritic arborization, prevent formation of autapses and allow free interaction among non-self neurons. Avoidance among self neurites is mediated by stochastic cell-surface expression of combinations of about 60 isoforms of α-, β- and γ-clustered protocadherin that provide mammalian neurons with single-cell identities. Avoidance is observed between neurons that express identical protocadherin repertoires, and single-isoform differences are sufficient to prevent self-recognition. Protocadherins form isoform-promiscuous cis dimers and isoform-specific homophilic trans dimers. Although these interactions have previously been characterized in isolation, structures of full-length protocadherin ectodomains have not been determined, and how these two interfaces engage in self-recognition between neuronal surfaces remains unknown. Here we determine the molecular arrangement of full-length clustered protocadherin ectodomains in single-isoform self-recognition complexes, using X-ray crystallography and cryo-electron tomography. We determine the crystal structure of the clustered protocadherin γB4 ectodomain, which reveals a zipper-like lattice that is formed by alternating cis and trans interactions. Using cryo-electron tomography, we show that clustered protocadherin γB6 ectodomains tethered to liposomes spontaneously assemble into linear arrays at membrane contact sites, in a configuration that is consistent with the assembly observed in the crystal structure. These linear assemblies pack against each other as parallel arrays to form larger two-dimensional structures between membranes. Furthermore, our results suggest that the formation of ordered linear assemblies by clustered protocadherins represents the initial self-recognition step in neuronal avoidance, and thus provide support for the isoform-mismatch chain-termination model of protocadherin-mediated self-recognition, which depends on these linear chains.
59 BASIC BIOLOGICAL SCIENCES↗
Multiomics and deep learning dissect regulatory syntax in human development
Transcription factors establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility and regulating gene expression1. Mapping accessible chromatin offers critical insights into transcriptional control, but available datasets for human development are restricted to bulk tissue, single organs or single modalities2. Here we present the Human Development Multiomic Atlas, a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types and more than 1 million candidate cis-regulatory elements, many of which exhibit organ-specific in vivo enhancer activity. Deep learning models trained to predict accessibility from local DNA sequence unravel a comprehensive lexicon of motifs that influence accessibility, including composite motifs exhibiting distinct syntactic constraints that are predicted to mediate transcription factor cooperativity. We identify ‘hard’ syntactic rules requiring precise motif spacing and orientation, ‘soft’ rules allowing flexible motif arrangements, and ubiquitous motifs inhibiting accessibility. Model-based interpretation of genetic variants reveals that disruption of motifs with positive and negative effects is associated with concordant effects on gene expression. Our work delineates how motif syntax governs cell-type-specific chromatin accessibility and provides a foundational resource for decoding cis-regulatory logic and interpreting genetic variation during human development.
59 BASIC BIOLOGICAL SCIENCES↗
Lignin Valorization: Two Hybrid Biochemical Routes for the Conversion of Polymeric Lignin into Value-added Chemicals
Naturally, many aerobic organisms degrade lignin-derived aromatics through conserved intermediates including protocatechuate and catechol. Employing this microbial approach offers a potential solution for valorizing lignin into valuable chemicals for a potential lignocellulosic biorefinery and enabling bioeconomy. In this study, two hybrid biochemical routes combining lignin chemical depolymerization, plant metabolic engineering, and synthetic pathway reconstruction were demonstrated for valorizing lignin into value-added products. In the biochemical route 1, alkali lignin was chemically depolymerized into vanillin and syringate as major products, which were further bio-converted into cis, cis-muconic acid (ccMA) and pyrogallol, respectively, using engineered Escherichia coli strains. In the second biochemical route, the shikimate pathway of Tobacco plant was engineered to accumulate protocatechuate (PCA) as a soluble intermediate compound. The PCA extracted from the engineered Tobacco was further converted into ccMA using the engineered E. coli strain. This study reports a direct process for converting lignin into ccMA and pyrogallol as value-added chemicals, and more importantly demonstrates benign methods for valorization of polymeric lignin that is inherently heterogeneous and recalcitrant. Our approach also validates the promising combination of plant engineering with microbial chassis development for the production of value added and speciality chemicals.
Science & Technology - Other Topics↗
The influence of proline isomerization on potency and stability of anti-HIV antibody 10E8
Monoclonal antibody (mAb) 10E8 recognizes a highly conserved epitope on HIV and is capable of neutralizing> 95% of circulating viral isolates making it one of the most promising Abs against HIV. Solution instability and biochemical heterogeneity of 10E8 has hampered its development for clinical use. We identify the source of 10E8 heterogeneity being linked to cis/trans isomerization at two prolines within the YPP motif in the CRD3 loop that exists as two predominant conformers that interconvert on a slow timescale. The Y trans P conformation conformer can bind the HIV gp41 epitope, while the Y cis P is not binding competent and shows a higher aggregation propensity. The high barrier of isomerization and propensity to adopt non-binding competent proline conformers provides novel insight into the slow binding kinetics, low potency, and poor solubility of 10E8. This study highlights how proline isomerization should be considered a critical quality attribute for biotherapeutics with paratopes containing potential cis proline amide bonds.
59 BASIC BIOLOGICAL SCIENCES↗
A rare terminal dinitrogen complex of chromium
Cis and trans-Cr–N₂ complexes supported by the diphosphine ligand P{sup Ph}₂N{sup Bn}₂ have been prepared. Positioned pendant amines in the second coordination sphere influence the thermodynamically preferred geometric isomer. Electronic structure calculations indicate negligible Cr–N₂ back-bonding; rather, electronic polarization of N₂ ligand is thought to stabilize Cr–N₂ binding.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular-ink route to 13.0% efficient low-bandgap CuIn(S,Se) 2 and 14.7% efficient Cu(In,Ga)(S,Se) 2 solar cells
A stable dimethyl sulfoxide (DMSO)-based ink containing a copper–thiourea–chloride complex and an indium–DMSO–chloride complex leads to 13.0% efficient CuIn(S,Se)2 (CIS) solar cells, which is a record for solution processed CIS. The formation of these complexes was found critical to control oxidation states and loss of metals during processing and to tailor the final composition of the absorber.
14 SOLAR ENERGY↗
Multiscale study of mononuclear Co II SMMs based on curcuminoid ligands
This work introduces a novel family of Co II species having a curcuminoid (CCMoid) ligand, 9Accm, attached, namely [Co(9Accm) 2 (py) 2 ] (1) and [Co(9Accm) 2 (2,2'-bpy)] (2), achieved in high yields by the use of a microwave reactor, and exhibiting two different arrangements for the 9Accm ligands, described as "cis"(2) and "trans"(1). The study of the similarities/differences of the magnetic, luminescent and surface behaviors of the two new species, 1 and 2, is the main objective of the present work. The determined single-crystal structures of both compounds are the only Co II -CCMoid structures described in the literature so far. Both compounds exhibit large positive D values, that of 1 (D = +74 cm -1 ) being three times larger than that of 2 (D = +24 cm -1 ), and behave as mononuclear Single-Molecule Magnets (SMMs) in the presence of an external magnetic field. Their similar structures but different anisotropy and SMM characteristics provide, for the first time, deep insight on the spin-orbital effects thanks to the use of CASSCF/NEVPT2 calculations implementing such contributions. Further magnetic studies were performed in solution by means of paramagnetic 1 H NMR, where both compounds (1 and 2) are stable in CDCl 3 and display high symmetry. Paramagnetic NMR appears to be a useful diagnostic tool for the identification of such molecules in solution, where the resonance values found for the methine group (-CH-) of 9Accm vary significantly depending on the cis or trans disposition of the ligands. Fluorescence studies show that both systems display chelation enhancement of quenching (CHEQ) with regard to the free ligand, while 1 and 2 display similar quantum yields. Deposition of 1-2 on HOPG and Si(100) surfaces using spin-coating was studied using AFM; UV photoemission experiments under the same conditions display 2 as the most robust system. The measured occupied density of states of 2 with UV photoemission is in excellent agreement with theoretical DFT calculations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Non-linear and non-local behaviour in spontaneously electrical solids
Using reflection–absorption infrared spectroscopy (RAIRS), we show that solids displaying spontaneous dipole orientation possess quite general non-local and non-linear characteristics, exemplified through their internal electric fields. The most graphic illustration of this, uncovered originally through electron beam studies, may be found in films of cis-methyl formate (cis-MF), for which data demonstrated the counter-intuitive property that the degree of dipole order in the film does not monotonically decrease as the temperature of deposition rises, but rather increases sharply above ~77 K. Here we show how RAIRS provides independent evidence to support this conclusion. These new data confirm (i) that the behaviour of spontelectrics is governed by an expression for the degree of dipole orientation, which is continuous in temperature, but with a discontinuity in the derivative, and (ii) that the temperature of deposition associated with this discontinuity matches the temperature above which dipole order switches from the expected reduction with temperature to an increase with temperature.
Roman, M.↗
Criegee intermediates and their impacts on the troposphere
We report Criegee intermediates (CIs), carbonyl oxides formed in ozonolysis of alkenes, play key roles in the troposphere. The decomposition of CIs can be a significant source of OH to the tropospheric oxidation cycle especially during nighttime and winter months. A variety of model-measurement studies have estimated surface-level stabilized Criegee intermediate (sCI) concentrations on the order of 1 × 10 4 cm -3 to 1 × 10 5 cm -3 , which makes a non-negligible contribution to the oxidising capacity in the terrestrial boundary layer. The reactions of sCI with the water monomer and the water dimer have been found to be the most important bimolecular reactions to the tropospheric sCI loss rate, at least for the smallest carbonyl oxides; the products from these reactions (e.g. hydroxymethyl hydroperoxide, HMHP) are also of importance to the atmospheric oxidation cycle. The sCI can oxidise SO 2 to form SO 3 , which can go on to form a significant amount of H 2 SO 4 which is a key atmospheric nucleation species and therefore vital to the formation of clouds. Lastly, the sCI can also react with carboxylic acids, carbonyl compounds, alcohols, peroxy radicals and hydroperoxides, and the products of these reactions are likely to be highly oxygenated species, with low vapour pressures, that can lead to nucleation and SOA formation over terrestrial regions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Biomass-derived monomers for performance-differentiated fiber reinforced polymer composites
Nearly all polymer resins used to manufacture critically important fiber reinforced polymer (FRP) composites are petroleum sourced. In particular, unsaturated polyesters (UPEs) are widely used as matrix materials and are often based on maleic anhydride, a four-carbon, unsaturated diacid. Typically, maleic anhydride is added as a reactant in a conventional step-growth polymerization to incorporate unsaturation throughout the backbone of the UPE, which is then dissolved in a reactive diluent (styrene is widely used) infused into a fiber mat and cross-linked. Despite widespread historical use, styrene has come under scrutiny due to environmental and health concerns; in addition, many conceivable UPEs are not soluble in styrene. In this study, we demonstrate that renewably-sourced monomers offer the ability to overcome these issues and improve overall composite performance. The properties of poly(butylene succinate)-based UPEs incorporating maleic anhydride are used as a baseline for comparison against UPEs derived from fumaric acid, cis , cis -muconate, and trans , trans -muconate, all of which can be obtained biologically. The resulting biobased UPEs are combined with styrene, methacrylic acid, or a mixture of methacrylic acid and cinnaminic acid, infused into woven fiberglass and cross-linked with the addition of a free-radical initiator and heat. This process produces a series of partially or fully bio-derived composites. Overall, the muconate-containing UPE systems exhibit a more favorable property suite than the maleic anhydride and fumaric acid counterparts. In all cases at the same olefinic monomer loading, the trans , trans -muconate polymers exhibit the highest shear modulus, storage modulus, and glass transition temperature indicating stronger and more thermally resistant materials. They also exhibit the lowest loss modulus indicating a greater adhesion to the glass fibers. The use of a mixture of methacrylic and cinnaminic acid as the reactive diluent results in a FRP composite with properties that can be matched to reinforced composites prepared with styrene. Significantly, at one-third the monomer loading (corresponding to two-thirds the number of double bonds), trans , trans -muconate produces approximately the same storage modulus and glass transition temperature as maleic anhydride, while exhibiting a superior loss modulus. Altogether, this work demonstrates the novel synthesis of performance-differentiated FRP composites using renewably-sourced monomers.
09 BIOMASS FUELS↗
Formaldehyde–isobutene Prins condensation over MFI-type zeolites
H-ZSM-5 was identified as the most efficient catalyst for the liquid phase Prins condensation of formaldehyde with isobutene to 3-methyl-3-buten-1-ol and subsequently isoprene.
Vasiliadou, Efterpi S.↗
Catalytic production of hexane-1,2,5,6-tetrol from bio-renewable levoglucosanol in water: effect of metal and acid sites on (stereo)-selectivity
In this article, we report on a new route to produce hexane-1,2,5,6-tetrol (tetrol) from cellulose-derived levoglucosanol (lgol). We investigate the reaction intermediates formed over metal and acid catalysts, and propose a reaction network for this process. Lgol is converted to tetrol in up to 90% yield over a bifunctional Pt/SiO 2 –Al 2 O 3 catalyst at 150 °C. High tetrol yields are maintained at lgol concentrations of up to 21 wt% in water. threo- and erythro-lgol first undergo hydrolysis to 3,4-dideoxymannose (DDM) and 3,4-dideoxyglucose (DDG), respectively. This reaction can be carried out selectively over an Amberlyst 70 acid catalyst at a temperature of 100 °C. At a higher temperature of 150 °C with no added catalyst, DDM and DDG undergo aldose–ketose isomerization to 3,4-dideoxyfructose (DDF). DDM is hydrogenated to cis-tetrol over a Pt/SiO 2 catalyst, while DDG is hydrogenated to trans-tetrol. Formation of DDF erases the stereocenter at the C 2 position of lgol, and hydrogenation of DDF produces a nearly 1:1 mixture of cis- and trans-tetrol. Lastly, this catalytic approach to produce tetrol from biomass opens the door to sustainable chemicals derived from tetrol.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Beyond the Coulson–Fischer point: characterizing single excitation CI and TDDFT for excited states in single bond dissociations
Linear response time dependent density functional theory (TDDFT), which builds upon configuration interaction singles (CIS) and TD-Hartree–Fock (TDHF), is the most widely used class of excited state quantum chemistry methods and is often employed to study photochemical processes. This paper studies the behavior of the resulting excited state potential energy surfaces beyond the Coulson–Fischer (CF) point in single bond dissociations, when the optimal reference determinant is spin-polarized. Many excited states exhibit sharp kinks at the CF point, and connect to different dissociation limits via a zone of unphysical concave curvature. In particular, the unrestricted M S = 0 lowest triplet T 1 state changes character, and does not dissociate into ground state fragments. The unrestricted M S = ±1 T 1 CIS states better approximate the physical dissociation limit, but their degeneracy is broken beyond the CF point for most single bond dissociations. On the other hand, the M S = ±1 T 1 TDHF states reach the asymptote too soon, by merging with the ground state from the CF point onwards. Use of local exchange–correlation functionals causes M S = ±1 T 1 TDDFT states to resemble their unphysical M S = 0 counterpart. The 2 orbital, 2-electron model system of minimal basis H 2 is analytically treated to understand the origin of these issues, revealing that the lack of double excitations is at the root of these remarkable observations. In conclusion, the behavior of excited state surfaces is also numerically examined for species like H 2 , NH 3 , C 2 H 6 and LiH in extended basis sets.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Generalized single excitation configuration interaction: an investigation into the impact of the inclusion of non-orthogonality on the calculation of core-excited states
In this paper, we investigate different non-orthogonal generalizations of the configuration interaction with single substitutions (CIS) method for the calculation of core-excited states. Fully non-orthogonal CIS (NOCIS) has been described previously for species with singlet and doublet ground states, and this paper reports the extension to molecules in their triplet ground state. In addition to NOCIS, we present a novel method, one-center NOCIS (1C-NOCIS), for open-shell molecules which is intermediate between NOCIS and the computationally less demanding static exchange approximation (STEX). We explore this hierarchy of spin-pure methods for core excitations of molecules with singlet, doublet, and triplet ground states. We conclude that, while NOCIS provides the best results and preserves the spatial symmetry of the wavefunction, 1C-NOCIS retains much of the accuracy of NOCIS at a dramatically reduced cost. For molecules with closed-shell ground states, STEX and 1C-NOCIS are identical.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗