bluuebunny/crossref_metadata_2025 huggingface dataset:
Resistive Pulse Sensing with Micro-fabricated Nanopores (NP-RPS) for Sub-micron Biomolecule and Bionanoparticle Analysis
Authors: LIU Ke
Published: February 2022

Biomolecules and bionanoparticles, such as nucleic acids, proteins, microorganisms and extracellular vesicles (EVs), are recognized as important targets for fundamental research, clinical diagnostic and therapeutic applications. To gain detailed information of those bionanoparticles, we demonstrate an electroosmotic (EO) driven transport behavior in silicon and silicon nitride-based nanopore, towards an accurate measure of concentration and sizing of sub-micro particles for a general biological interest.
Mechanochemical Grignard Reactions with Gaseous CO2 and Sodium Methyl Carbonate
Authors: Pfennig Victoria , Villella Romina , Nikodemus Julia , Bolm Carsten
Published: February 2022

Grignard reactions invert the intrinsic electrophilic reactivity of organohalides to form C–C bonds with other electrophiles. With carbon dioxide (CO2) as electrophile carboxylic acids can be prepared. Although scattered examples of mechanochemical reactions with CO2 have been reported, its synthetic application as C1-synthon has remained underexplored. Here, we developed a one-pot three-step protocol for the preparation of Grignard reagents from organobromides in a ball mill and their subsequent reaction with gaseous CO2 or sodium methyl carbonate to provide aryl and alkyl carboxylic acids in up to 82% yield. Noteworthy are the short reaction times and the significantly reduced solvent amount [2.0 equiv. for liquid assisted grinding (LAG) conditions]. Unexpectedly, aryl bromides with methoxy substituents lead to symmetric ketones as major products.
Conformation and supramolecular arrangement of 1,3:2,4-dibenzyli-dene-D-sorbitol in solution and in single crystals
Authors: Berride Fernán , Sánchez-Pedregal Victor M. , Dacuña Bruno , Cabrita Eurico , Navarro-Vázquez Armando , Weiss Richard G. , Cid María Magdalena
Published: February 2022

The X-ray crystal structure of the gelator 1,3:2,4-dibenzylidene-D-sorbitol (DBS) is reported here. DBS is an important gelating molecule known for nearly 130 years, that has eluded crystallization until now. The crystal obtained presents an axial stacking of DBS molecules stabilized by both Van der Waals interactions and intermolecular hydrogen bonds of the side chain hydroxyl groups with either neighboring DBS or water molecules. The crystal structure shows definitive evidence for the frequently assumed “butterfly” type aggregation mode and experimentally proves the equatorial placement of the phenyl rings. The conformation of DBS has been analyzed in the crystal structure and compared with that determined in solution through NMR spectroscopy.
Aluminum Foil Anodes for Li-ion Rechargeable Batteries: The Role of Li Solubility within β-LiAl
Authors: Zheng Tianye , Kramer Dominik , Mönig Reiner , Boles Steven
Published: February 2022

Li-ion battery (LIB) electrodes contain a substantial amount of electrochemically inactive materials, including binder, conductive agent, and current collectors. These extra components significantly dilute the specific capacity of whole electrodes, and thus have led to efforts to utilize foils, e.g., Al, as the sole anode material. Interestingly, the literature has many reports of fast degradation of Al electrodes, where less than a dozen cycles can be achieved. However, in some studies, Al anodes demonstrate stable cycling life with several hundred cycles. In this work, we present a successful pathway for enabling long-term cycling of simple Al foil anodes: β-LiAl phase grown from Al foil (α-Al) exhibits a cycling life of 500 cycles with a ~96% capacity retention when paired with a commercial cathode. The excellent performance stems from strategic utilization of the Li solubility range of β-LiAl that can be (de-)lithiated without altering its crystal structure. This solubility range at room temperature is determined to be ~6 at%. Consequently, this design circumvents the critical issues associated with the α/β/α phase transformations, such as volume change, mechanical strain, and nanopore formation. Application-wise, the maturity of aluminum industry, combined with excellent sustainability prospects, makes this anode an important option for future devices.
Patterned crystal growth and heat wave generation in hydrogels
Authors: Schroeder Thomas B. H. , Aizenberg Joanna
Published: February 2022

The crystallization of metastable liquid “phase change materials” releases stored energy as latent heat upon nucleation and may therefore provide a triggerable means of activating downstream processes that respond to changes in temperature. In this work, we describe a strategy for controlling the fast, exothermic crystallization of sodium acetate from a metastable aqueous solution into trihydrate crystals within a polyacrylamide hydrogel whose polymerization state has been patterned using photomasks. A comprehensive experimental study of crystal shapes, crystal growth front velocities and evolving thermal profiles showed that rapid growth of long needle-like crystals through unpolymerized solutions produced peak temperatures of up to 45˚C, while slower-crystallizing polymerized solutions produced polycrystalline composites and peaked at 30˚C due to lower rates of heat release relative to dissipation in these regions. This temperature difference and propagating heat waves, which we describe using a proposed analytical model, enable the use of this strategy to selectively activate thermoresponsive processes in predefined areas.
Diarylation of N- and O-nucleophiles through a metal-free cascade reaction
Authors: Linde Erika , Bulfield David , Kervefors Gabriella , Purkait Nibadita , Olofsson Berit
Published: February 2022

The arylation of heteroatom nucleophiles is a central strategy to reach diarylated compounds that are key building blocks in agrochemicals, materials and pharmaceuticals. Nucleophilic aromatic substitution is a classical tool for such arylations, and hypervalent iodine-mediated arylations are modern alternatives to achieve a wider scope of products. Herein, we combine the benefits of those strategies to enable an atom-efficient and transition metal-free functionalization of N- and O- nucleophiles with two structurally different aryl groups, to provide di- and triarylamines and diaryl ethers in one single step (> 100 examples). The core of this strategy is the unique reactivity discovered with certain fluorinated diaryliodonium salts, which unveils novel reaction pathways in hypervalent iodine chemistry. The method is suitable for aliphatic amines, anilines, ammonia and even water and tolerates a wide variety of functional and protecting groups. Furthermore, the retained iodine substituent is easily accessible for derivatization of the products.
Room temperature hydrolysis of benzamidines and benzamidiniums in weakly basic water
Authors: Yu Lijuan , Cullen Duncan , Morshedi Mahbod , Coote Michelle , White Nicholas
Published: February 2022

Benzamidinium compounds have found widespread use in both medicinal and supramolecular chemistry. In this work, we show that benzamidiniums hydrolyse at room temperature in aqueous base to give the corresponding primary amide. This reaction has a half-life of 300 days for unsubstituted benzamidinium at pH 9, but is relatively rapid at higher pHs (e.g. t1/2 = 6 days at pH 11 and 15 hours at pH 13). Quantum chemistry combined with first principles kinetic modelling can reproduce these trends and explain them in terms of the dominant pathway being initiated by attack of HO– on benzamidine. Incorporation of the amidinium motif into a hydrogen bonded framework offers a substantial protective effect against hydrolysis.
Viscose-derived activated carbons fibers as highly efficient adsorbents for dimethoate removal from water
Authors: Jocic Ana , Breitenbach Stefan , Bajuk-Bogdanović Danica , Pašti Igor , Unterweger Christoph , Fürst Christian , Lazarević-Pašti Tamara
Published: February 2022

Extensive use of pesticides resulting in their accumulation in the environment presents a hazard for their non-target species, including humans. Hence, efficient remediation strategies are needed, and adsorption is seen as the most straightforward approach in this sense. We have studied activated carbon fibers (ACFs) derived from viscose fibers impregnated with diammonium hydrogen phosphate (DAHP). By changing the amount of DAHP in the impregnation step, the chemical composition and textural properties of ACFs are effectively tuned, affecting their performance for dimethoate removal from water. The prepared ACFs effectively reduced the toxicity of treated water samples, both deionized water solutions and spiked tap water samples, under batch conditions and in dynamic filtration experiments. Using the results of physicochemical characterization and dimethoate adsorption measurements, multiple linear regression models were made to predict performance towards dimethoate removal from water reliably. These models can be used to quickly screen among larger sets of possible adsorbents and guide the development of novel, highly efficient adsorbents for dimethoate removal from water.
Molecular understanding of GPR120 agonist binding using homology modeling and molecular dynamics
Authors: pant suyash , Ravichandiran V
Published: February 2022

The toll of type-2 diabetes and associated complications are continues, efforts to identify possible targets are ongoing. Free fatty acid receptor 4 (FFAR4/GPR120) has been recently identified to be a promising therapeutic target for a group of metabolic associated disorders. For the prevention of type 2 diabetes, significant scientific and commercial interest has been developed around GPR120 and its role. Due to the unavailability of a crystal structure, the interaction dynamics of GPR120 agonists were not yet determined to date. In the present study, we constructed the homology model for GPR120 and validated using available mutational data and molecular dynamics simulation, and explored its binding modes with known small molecule agonists. So, sixteen propionic acid derivatives as GPR120 agonists were collected to elucidate their binding modes. Experiential and theoretical studies suggested that the carboxylic group of ligands interact with Arg99, which is an important interaction for GPR120 activation. However, earlier reports also suggest that this interaction is not stable during the molecular dynamics simulation, which contradicts the experimental observations. Evidently, to refute this, we got a stable interaction of Arg99 with TUG891 and other recently reported 15 GPR120 agonists. In addition, we have also observed that in 1 µs molecular dynamics simulation Arg183 present in ECL2 tends to come inside and interact with ligand. Molecular dynamics simulation study provides a list of key hotspot residues which play an important role in ligand binding. The homology model and results provides could be further utilized as a powerful template to accelerate the research in this field.
Magnesium-Stabilised Transition Metal Formyl Complexes: Structures, Bonding, and Ethenediolate Formation
Authors: Parr Joe , White Andrew J. P. , Crimmin Mark
Published: February 2022

Herein we report the first comprehensive series of crystallographically characterised transition metal formyl complexes. In these complexes, the formyl ligand is trapped as part of a chelating structure between a transition metal (Cr, Mn, Fe, Co, Rh, W, and Ir) and a magnesium (Mg) cation. Calculations suggest that this bonding mode results in significant oxycarbene-character of the formyl ligand. Electron-rich late-transition metal complexes have the highest oxycarbene-character to the bonding and are the most stable in solution. Further reaction of a heterometallic Cr---Mg formyl complex results in a rare example of C–C coupling and formation of an ethenediolate complex. These results show that well-defined transition metal formyl complexes are potential intermediates in the homologation of carbon monoxide.
Ball Milling Enabled Reactivity of Manganese Metal
Authors: Browne Duncan , Nicholson William , Howard Joseph , Magri Giuseppina , Seastram Alex , Khan Adam , Morrill Louis , Richards Emma
Published: February 2022

Efforts to generate organomanganese reagents under ball milling conditions have led to the serendipitous discovery that manganese metal can mediate the reductive dimerization of arylidene malonates. The newly uncovered process has been optimized and its mechanism explored using CV measurements, radical trapping experiments, EPR spectroscopy and solution control reactions. This unique reactivity can also be translated to solution where upon pre-milling of the manganese is required.
Carbonate-Catalyzed Reverse Water-Gas Shift to Produce Gas Fermentation Feedstocks for Renewable Liquid Fuel Synthesis
Authors: Li Chastity , Frankhouser Amy , Kanan Matthew
Published: February 2022

Carbon-neutral liquid fuel generation is essential for decarbonizing sectors that cannot readily electrify. Recently commercialized acetogenic gas fermentation offers an alternative to conventional biofuels that circumvents efficiency limitations and land requirements, provided the requisite H2/CO feedstocks can be generated efficiently using renewable inputs. CO2 electrolysis to CO is under development for this purpose, but suffers from scalability challenges and impurity sensitivity. We describe an alternative that utilizes dispersed alkali carbonates as reverse water-gas shift (RWGS) catalysts to convert H2 and CO2 to an appropriate ratio of CO/CO2/H2 for acetogenic fermentation. Using a fixed bed reactor operating at industrially relevant space velocity, we demonstrate equilibrium RWGS conversion starting at 410 °C that remains stable over days, even with 50 ppm H2S impurity. The combination of carbonate-catalyzed RWGS, water electrolysis, and gas fermentation could convert electricity to ethanol with nearly 50% energy efficiency, providing a compelling option for renewable liquid fuel production.
The Sea Spray Chemistry and Particle Evolution Study (SeaSCAPE): Overview and Experimental Methods
Authors: Sauer Jonathan , Mayer Kathryn , Lee Christopher , Alves Michael , Amiri Sarah , Bahaveolos Cristina , Barnes Emily , Crocker Daniel , Dinasqauet Julie , Garofalo Lauren , Kaluarachchi Chathuri , Dang Duyen , Kilgour Delaney , Mael Liora , Mitts Brock , Moon Daniel , Morris Clare , Moore Alexia , Ni Chi-min , Pendergraft Matthew , Petras Daniel , Simpson Rebecca , Smith Stephanie , Tumminello Paul , Walker Joseph , Demott Paul , Farmer Delphine , Goldstein Allen , Grassian Vicki , Jaffe Jules , Malfatti Francesca , Martz Todd , Slade Jonathan , Tivanski Alexei , Bertram Timothy , Cappa Christopher , Prather Kimberly
Published: February 2022

Marine aerosols strongly influence climate through their interactions with solar radiation and clouds. However, significant questions remain regarding the influences of biological activity and seawater chemistry on the flux, chemical composition, and climate-relevant properties of marine aerosols and gases. Wave channels, a traditional tool of physical oceanography, have been adapted for large-scale ocean-atmosphere mesocosm experiments in the laboratory. These experiments enable the study of aerosols under controlled conditions which isolate the marine system from atmospheric anthropogenic and terrestrial influences. Here, we present an overview of the 2019 Sea Spray Chemistry and Particle Evolution (SeaSCAPE) study, which was conducted in an 11,800 L wave channel which was modified to facilitate atmospheric measurements. The SeaSCAPE campaign sought to determine the influence of biological activity in seawater on the production of primary sea spray aerosols, volatile organic compounds (VOCs), and secondary marine aerosols. Notably, the SeaSCAPE experiment also focused on understanding how photooxidative aging processes transform the composition of marine aerosols. In addition to a broad range of aerosol, gas, and seawater measurements, we present key results which highlight the experimental capabilities during the campaign, including the phytoplankton bloom dynamics, VOC production, and the effects of photochemical aging on aerosol production, morphology, and chemical composition. Additionally, we discuss the modifications made to the wave channel to improve aerosol production and reduce background contamination, as well as subsequent characterization experiments. The SeaSCAPE experiment provides unique insight into the connections between marine biology, atmospheric chemistry, and climate-relevant aerosol properties, and demonstrates how an ocean-atmosphere-interaction facility can be used to isolate and study reactions in the marine atmosphere in the laboratory under more controlled conditions.
On the value of using 3D-shape and electrostatic similarities in deep generative methods
Authors: Bolcato Giovanni , Boström Jonas
Published: February 2022

Multi-parameter optimization, the heart of drug design, is still an open challenge. Thus, improved methods for automated compounds design with multiple controlled properties are desired. Here, we present a significant extension to our previously described fragment-based reinforcement learning method (DeepFMPO) for the generation of novel molecules with optimal properties. As before, the generative process outputs optimized molecules similar to the input structures, now with the improved feature of replacing parts of these molecules with fragments of similar 3D-shape and electrostatics. By performing comparisons of 3D-fragments, we can simulate 3D properties while overcoming the notoriously difficult step of accurately describing bioactive conformations. The comparison of electrostatic potential and molecular shape is performed using the new ESP-Sim python package, allowing the calculation of state-of-the-art partial charges (e.g., RESP with B3LYP/6-31G**) obtained using the quantum chemistry program Psi4. The new improved method is demonstrated with a scaffold-hopping exercise identifying CDK2 bioisosteres. All code is open-source and freely available.
Double Heterohelicenes Composed of Benzo[b]- and Dibenzo[b,i]phenoxazine: A Comprehensive Comparison of Their Electronic and Chiroptical Properties
Authors: Sakamaki Daisuke , Tanaka Shunya , Tanaka Katsuki , Takino Mayu , Gon Masayuki , Tanaka Kazuo , Hirose Takashi , Hirobe Daichi , Yamamoto Hiroshi M. , Fujiwara Hideki
Published: February 2022

Heterohelicenes are potential materials in molecular electronics and optics because of their inherent chirality and various electronic properties originating from the introduced heteroatoms. In this work, we comprehensively investigated two kinds of double NO-hetero[5]helicenes composed of 12H-benzo[b]phenoxazine (BPO) and 13H-dibenzo[b,i]phenoxazine (DBPO). Both heterohelicenes were easily synthesized by oxidative dimerization of BPO or DBPO followed by the oxidative ring fusion, and the yield of BPO-double heterohelicene was much improved compared to the previously reported DBPO-analogue. These helicenes exhibit good electron donor property reflecting the electron-rich character of their monomers and were demonstrated to work as p-type semiconductors. The enantiomers of these helicenes do not racemize at room temperature and show the largest class of dissymmetry factors for circularly polarized luminescence (CPL) (|gCPL| > 10−2) among the previously reported helicenes. Interestingly, the signs of CPL are opposite between BPO- and DBPO-double helicenes of the same helicity. The origin of the large gCPL values and the inversion of the CPL signs was addressed by analysis of the transition electronic dipole moments (TEDM) and transition magnetic dipole moments (TMDM) based on the TD-DFT calculations.
Double Heterohelicenes Composed of Benzo[b]- and Dibenzo[b,i]phenoxazine: A Comprehensive Comparison of Their Electronic and Chiroptical Properties
Authors: Sakamaki Daisuke , Tanaka Shunya , Tanaka Katsuki , Takino Mayu , Gon Masayuki , Tanaka Kazuo , Hirose Takashi , Hirobe Daichi , Yamamoto Hiroshi M. , Fujiwara Hideki
Published: February 2022

Heterohelicenes are potential materials in molecular electronics and optics because of their inherent chirality and various electronic properties originating from the introduced heteroatoms. In this work, we comprehensively investigated two kinds of double NO-hetero[5]helicenes composed of 12H-benzo[b]phenoxazine (BPO) and 13H-dibenzo[b,i]phenoxazine (DBPO). These helicenes exhibit good electron donor property reflecting the electron-rich character of their monomers and were demonstrated to work as p-type semiconductors. The enantiomers of these helicenes show the largest class of dissymmetry factors for circularly polarized luminescence (CPL) (|gCPL| > 10−2) among the previously reported helicenes. Interestingly, the signs of CPL are opposite between BPO- and DBPO-double helicenes of the same helicity. The origin of the large gCPL values and the inversion of the CPL signs was addressed by analysis of the transition electronic dipole moments (TEDM) and transition magnetic dipole moments (TMDM) based on the TD-DFT calculations.
Charge Induced Chi(3) Susceptibility in Interfacial Nonlinear Optical Spectroscopy Beyond the Bulk Aqueous Contributions: The Case for Silica/Water Interface
Authors: Wang Hui , Hu Xiaohua , Wang Hongfei
Published: February 2022

The electric field induced (EFI) bulk Chi(3) contribution to the second harmonic generation (SHG) signal from charged interfaces was discovered and applied to study the interfacial chemistry of various charged interfaces three decades ago. For both the buried fused silica/water interface and the exposed charged monolayer covered air/water interface, such bulk Chi(3) contribution was all attributed to the Chi(3) term of the polarized water molecules near the charged interfaces. The puzzling experimental observation of the more than one-order of magnitude difference of the EFISHG intensity between the fully charged silica/water interface and the charged molecular covered air/water interface was generally overlooked in the EFISHG literature. Nevertheless, this significant signal difference suggests additional source for the Chi(3) contribution at the fully charged silica/water interface other than the polarized water molecules as in the case of charged monolayer covered air/water interface. In this report, we re-examine the treatment of the Chi(3) mechanism at the charged silica/water interface by including the contributions from the bulk silica using proper boundary condition and image charge distributions for the change screening effects inside bulk silica phase. We show that the Chi(3) contribution from the bulk silica is in similar form as that of the aqueous bulk phase, and it is with more than one-order of magnitude and with opposite sign. The treatment reported here can be extended to other charged interfaces.
Selective binding of small molecules to Vibrio cholerae DsbA offers a starting point for the design of novel antibacterials
Authors: Wang Geqing , Mohanty Biswaranjan , Williams Martin , Doak Bradley , Dhouib Rabeb , Totsika Makrina , Macmahon Róisín , Sharma Gaurav , Zheng Dan , Bentley Matthew , Chin Yanni Ka-Yan , Horne James , Chalmers David , Heras Begona , Scanlon Martin
Published: February 2022

DsbA enzymes catalyze oxidative folding of proteins that are secreted into the periplasm of Gram-negative bacteria, and they are indispensable for the virulence of human pathogens such as Vibrio cholerae and Escherichia coli. Therefore, targeting DsbA represents an attractive approach to control bacterial virulence. X-ray crystal structures reveal that DsbA enzymes share a similar fold, however, the hydrophobic groove adjacent to the active site, which is implicated in substrate binding, is shorter and flatter in the structure of V. cholerae DsbA (VcDsbA) compared to E. coli DsbA (EcDsbA). The flat and largely featureless nature of this hydrophobic groove is challenging for the development of small molecule inhibitors. Using fragment-based screening approaches, we have identified a novel small molecule, based on the benzimidazole scaffold, that binds to the hydrophobic groove of oxidized VcDsbA with a KD of 446 ± 10 µM. The same benzimidazole compound has ~8-fold selectivity for VcDsbA over EcDsbA and binds to oxidized EcDsbA, with KD > 3.5 mM. We generated a model of the benzimidazole complex with VcDsbA using NMR data but were unable to determine the structure of the benzimidazole bound EcDsbA using either NMR or X-ray crystallography. Therefore, a structural basis for the observed selectivity is unclear. To better understand ligand binding to these two enzymes we crystallized each of them in complex with a known ligand, the bile salt sodium taurocholate. The crystal structures show that taurocholate adopts different binding poses in complex with VcDsbA and EcDsbA, and reveals the protein-ligand interactions that stabilize the different modes of binding. This work highlights the capacity of fragment-based drug discovery to identify inhibitors of challenging protein targets. In addition, it provides a starting point for development of more potent and specific VcDsbA inhibitors that act through a novel anti-virulence mechanism.
The Volumetric Properties of the Transition State Ensemble for Protein Folding
Authors: Avagyan Samvel , Makhatadze George
Published: February 2022

Hydrostatic pressure together with the temperature is an important environmental variable that plays an essential role in biological adaptation of extremophilic organisms. In particular, the effects of hy-drostatic pressure on the rates of the protein folding/unfolding reaction are determined by the magni-tude and sign of the activation volume changes. Here we provide computational description of the ac-tivation volume changes for folding/unfolding reaction, and compare them with the experimental data for six different globular proteins. We find that the volume of the transition state ensemble is always in-between the folded and unfolded states. Based on this, we conclude that hydrostatic pressure will invariably slow down protein folding and accelerate protein unfolding.
High Spin Cobalt Complexes Supported by a Trigonal Tris(Phosphinimide) Ligand
Authors: Lee Heui Beom , Ciolkowski Nicholas , Winslow Charles , Rittle Jonathan
Published: February 2022

Terminal, π-basic moieties occupy a prominent position in the stabilization of unusual or reactive inorganic species. The electron-releasing, π-basic properties of phosphinimides have been employed to stabilize electron deficient early transition metals and lanthanides. In principle, a ligand field comprised of terminal PN groups should enable access to high-valent states of late first row transition metals. Herein, we report a new class of multidentate phosphinimide ligands to logically explore this hypothesis. Access to such ligands is made possible by a new procedure for the electrophilic amination of rigid, sterically-encumbering, multidentate phosphines. Such frameworks facilitate terminal PN coordination to Cobalt as demonstrated by the synthesis of a three-coordinate CoIII complex, which exhibits an exceedingly rare S = 2 ground state. Combined XRD, magnetic susceptibility, and DFT studies highlight that terminally-bound PNs engage in strong dπ-pπ interactions that present a weak ligand field appropriate to stabilize high-spin states of late transition metals.
Non-enzymatic degradation of carbon nanotubes in the presence of bacterial enzymes
Authors: Hori Katsutoshi , Takahashi Seira , Taguchi Fumiko
Published: February 2022

The enzymatic degradation of carbon nanotubes (CNTs) by several enzymes has been reported. However, because organisms that possess these enzymes have limited habitats and distribution areas, it is unclear whether CNTs can be degraded in the general environment. The investigation of CNTs degradation by enzymes derived from bacteria, which inhabit a wide range of environments and have diverse metabolic systems, is inevitable for predicting the environmental fate of CNTs. In this study, the degradation of oxidized (carboxylated) single-walled CNTs (O-SWCNTs) by mt2DyP, a dye-decolorizing peroxidase of Pseudomonas putida mt-2, a common soil bacterium, was investigated. Suspensions of O-SWCNTs gradually became transparent and their optical absorbance decreased during 30 d of incubation in the presence of mt2DyP produced by a recombinant Brevibacillus choshinensis strain and its substrate, H2O2. The degradation was enhanced by higher H2O2 concentrations. The measurement of Raman spectra revealed the complete degradation of O-SWCNTs after 30 d of incubation with 100 mM H2O2. However, surprisingly, this heme enzyme was inactivated within 60 min of the incubation with O-SWCNTs, which suggested that the degradation of O-SWCNTs was not catalyzed by the enzyme. The inactivation of mt2DyP was accompanied by the release of iron, which suggested that the degradation of the O-SWCNTs was owing to the Fenton reaction caused by the iron released from mt2DyP and the supplied H2O2. A chelating agent, diethylenetriaminepentaacetic acid, significantly inhibited the O-SWCNTs degradation, proving the degradation by the Fenton reaction. These phenomena were also observed with another heme enzyme, Cytochrome P450. These results are important for predicting the fate of CNTs in a wide range of environments, as heme enzymes are secreted by many bacteria in the environment. This study also shows that the effect of the Fenton reaction should be considered to validate the degradation of CNTs by heme enzymes.
Electrochemical cobalt-catalyzed selective carboxylation of benzyl halides with CO2 enabled by low-coordinate cobalt electrocatalysts
Authors: Malapit Christian , Tanwar Mayank , Pendergast Andrew , Udyavara Sagar , Beck Wesley , Smith Ryan , Kadic Selma , Primo Tommy , Wu Ding , Stone Tanner , White Henry , Neurock Matthew , Sigman Matthew , Minteer Shelley
Published: February 2022

The direct, transition metal-catalyzed carboxylation of organohalides with carbon dioxide is a highly desirable transformation in organic synthesis as it utilizes feedstock chemicals and delivers carboxylic acids –among the most utilized class of organic molecules. Phenyl acetic acids, in particular, are privileged motifs that appear in many pharmaceuticals and biologically active compounds. This article reports the development of a sustainable and selective cobalt-catalyzed electrochemical carboxylation of benzyl halides with CO2 to generate phenyl acetic acids. The success of this transformation is enabled by the development of low-coordinate cobalt/pyrox complexes as electrocatalysts to convert various benzyl chlorides and bromides to their corre-sponding phenyl/heteroaryl acetic acids with high selectivity over undesired homocoupling of the benzyl halides. The combina-tion of electroanalytical methods, simulation studies, control reactions, and first-principles density functional theory (DFT) calculations informed the mechanistic analysis of this reaction. An EC’C-type activation mechanism of benzyl halides, which is unique to Co(II)/pyrox electrocatalysts, provides the rationalization of the exceptional observed selectivity for carboxylation. Specifically, the Co(II)/pyrox catalyst undergoes reduction to Co(I) followed by halogen abstraction and a favorable radical rebound to Co(II)/pyrox to form alkyl–Co(III) intermediates. Although voltammetry only shows a single electron transfer step, bulk electrolysis shows a two electron process and using DFT calculations, the intermediates are proposed to undergo two-electron reduction to alkyl–Co(I) followed by a ZnCl2-assisted CO2 insertion to form the carboxylated adducts with regenera-tion of Co(I)/pyrox.
Pre- and post-industrial levels of polycyclic aromatic hydrocarbons in sediments from the Estuary and Gulf of St. Lawrence (eastern Canada)
Authors: Corminboeuf Anne , Montero-Serrano Jean-Carlos , St-Louis Richard , Dalpé Allyson , Gélinas Yves
Published: February 2022

The concentrations of 23 polycyclic aromatic hydrocarbons (PAHs; 16 parent PAHs and 7 alkyl-PAHs) were determined in 45 surface sediment and 7 basal sediment box core samples retrieved from the Estuary and Gulf of St. Lawrence in eastern Canada. The concentration sums of 16 priority PAHs (Σ16PAHs) in the surface sediments ranged from 71 to 5672 ng g−1. Σ16PAHs in the basal sediments ranged from 93 to 172 ng g−1 among the pre-industrial samples and from 1216 to 1621 ng g−1 among the early post-industrial samples. The highest Σ16PAH values occurred in samples retrieved from the Baie-Comeau-Matane area, an area affected by intense industrial anthropogenic activities. Source-diagnostic PAH ratios suggest a predominance of pyrogenic sources via atmospheric deposition, with a minor contribution of petrogenic seabed pockmark sources. The PAH concentrations in the sediments from the study areas reveal low ecological risks to benthic or other organisms living near the water-sediment interface.
Chiral Diamine in Small Molecule Biomimetic Asymmetric Catalysis
Authors: Zeng Fanyun , Chen Chen , Liu Liu , Li Yifan , Li Bo , Lin Guotao , Huang Shihao , Zhang Mingyu , Yan Yuting , Zhang Yuan , Dang Yanfeng , Huang Jianhui
Published: February 2022

Enzymatic reaction, as an environmentally friendly approach, has made great progress producing commodity chemicals comparing to the conventional metallo/organo catalysis. However, the reaction compatibility is not satisfactory. The development of biomimetic catalysis balancing both strategies for the green and broad application in synthesis is desirable. Here, we report the design and synthesis of a chiral diamine catalyst fulfilling this requirement. Asymmetric addition reactions using this ligand in water were demonstrated and the corresponding products were produced in excellent yields and enantiomeric ratios. This pluripotent ligand has also shown good reactivity/enantioselectivity on a number of representative reactions in both green and organic solvents. We anticipate that the ligand would allow further development of other catalysts for important yet challenging green stereoselective transformations.
Dual-functional cobalt catalyst enables electrocatalytic allylic C–H alkylation
Authors: Chen Ming , Wu Zheng-Jian , Xu Hai-Chao
Published: February 2022

Transition metal-catalyzed allylic substitution reactions of pre-activated allylation agents with nucleophiles are extensively studied synthetic methods that have enjoyed widespread applications in organic synthesis. The direct alkylation of allylic C–H bonds with nucleophiles, which minimizes pre-functionalization and converts inexpensive, abundantly available materials to value-added alkenyl-substituted products, remains challenging. Current methods generally involve C–H activation, require the use of noble-metal catalysts and stoichiometric chemical oxidants, and often show limited scope. Here we report an electrocatalytic allylic C–H alkylation reaction with carbon nucleophiles employing an easily available cobalt-salen complex as the molecular catalyst. These C(sp3)–H/C(sp3)–H cross-coupling reactions proceed through H2 evolution and require no external chemical oxidants. Importantly, the mild conditions and radical mechanism ensure excellent functional group tolerance and substrate compatibility with both linear and branched terminal alkenes. The synthetic utility of the electrochemical method is highlighted by its scalability (up to 200 mmol scale) and its successful application in the late-stage functionalization of complex structures.
Low Energy Carbon Capture via Electrochemically Induced pH Swing with Electrochemical Rebalancing
Authors: Jin Shijian , Wu Min , Jing Yan , Gordon Roy , Aziz Michael
Published: February 2022

We demonstrate a carbon capture system based on pH swing cycles driven through proton-coupled electron transfer of sodium (3,3’-(phenazine-2,3-diylbis(oxy))bis(propane-1-sulfonate)) (DSPZ) molecules. Electrochemical reduction of DSPZ causes an increase of hydroxide concentration, which absorbs CO2; subsequent electrochemical oxidation of the reduced DSPZ consumes the hydroxide, causing CO2 outgassing. The measured electrical work of separating CO2 from a binary mixture with N2, at CO2 inlet partial pressures ranging from 0.1 to 0.5 bar, and releasing to a pure CO2 exit stream at 1.0 bar, was measured for electrical current densities of 20 to 150 mA/ cm2. The work for separating CO2 from a 0.1 bar inlet and concentrating into 1 bar exit is 61.3 kJ/molCO2 at a current density of 20 mA/cm2 and extrapolates to 57.1 kJ/molCO2 in the low-current-density limit. At this limit, the cycle work for capture from 0.4 mbar extrapolates to 108-212 kJ/ molCO2 depending on the initial composition of the electrolyte. We also introduce an electrochemical rebalancing method that extends cell lifetime by recovering the initial electrolyte composition after it is perturbed by side reactions. We discuss the implications of these results for future low-energy electrochemical carbon capture devices.
Sequence-complementarity dependent co-assembly of phosphodiester-linked aromatic donor-acceptor trimers
Authors: Appukutti Nadeema , de Vries Alex , Gudeangadi Prashant , Claringbold Bini , Garrett Michelle , Reithofer Michael , Serpell Christopher
Published: February 2022

Development of the interplay between monomer sequence and supramolecular chemistry is critical if chemistry is to recapitulate the properties of proteins and nucleic acids in the synthetic world. We have created sequenced trimers of aromatic donor/acceptor units which participate in charge-transfer interactions, linked by phosphodiesters. Each sequence displays its own characteristic self-assembly, and moreover complementary sequences interact with each other to produce new nanostructures and emergent thermochromism. This finding paves the way towards new functional nanomaterials which make bio-analogous use of sequence to tune structure.
Nitrogen K-edge X-ray absorption Spectra of Ammonium and Ammonia in Water Solution: Assessing the Performance of Polarizable Embedding Coupled Cluster Methods
Authors: Reinholdt Peter , Vidal Marta L. , Kongsted Jacob , Iannuzzi Marcella , Coriani Sonia , Odelius Michael
Published: February 2022

As X-ray absorption measurements of solutes in liquid environment become increasingly accessible, there is a strong need for reliable theoretical methods to assist in the interpretation of the experimental data. Coupled cluster (CC) methods, considered among the most accurate tools in electronic structure theory to obtain molecular properties and spectra, have been extensively developed over the last decade to simulate X-ray absorption in the gas phase. Their performance for solvated species, on the other hand, has remained so far largely unexplored. Here, we investigate the current state of the art of CC modeling of N K-edge X-ray absorption of aqueous ammonia and ammonium, based on various levels of QM/MM. Both the level of CC calculations and polarizable embedding are scrutinized. The results are compared to existing experimental data as well as simulations based on transition-potential density functional theory results.
Metal-organic frameworks as hypergolic additives for hybrid rockets
Authors: Jobin Olivier , Mottillo Cristina , Titi Hatem M. , Marrett Joseph M. , Arhangelskis Mihails , Rogers Robin D. , Elzein Bachar , Friščić Tomislav , Robert Étienne
Published: February 2022

Hybrid rocket propulsion can contribute to reduce launch costs by simplifying engine design and operation. Hypergolic propellants, i.e. igniting spontaneously and immediately upon contact between fuel and oxidizer, further simplify system integration by removing the need for an ignition system. Such hybrid engines could also replace currently popular hypergolic propulsion approaches based on extremely toxic and carcinogenic hydrazines. Here we present the first demonstration for the use of hypergolic metal-organic frameworks (HMOFs) as additives to trigger hypergolic ignition in conventional paraffin-based hybrid engine fuels. HMOFS are a recently introduced class of stable and safe hypergolic materials, used here as a platform to bring readily tunable ignition and combustion properties to hydrocarbon fuels. We present an experimental investigation of the ignition delay (ID, the time from first contact with an oxidizer to ignition) of blends of HMOFs with paraffin, using White Fuming Nitric Acid (WFNA) as the oxidizer. The majority of measured IDs are under 10 ms, significantly below the upper limit of 50 ms required for functional hypergolic propellant, and within the ultrafast ignition range. A theoretical analysis of the performance of HMOFs-containing fuels in a hybrid launcher engine scenario also reveals the effect of the HMOF mass fraction on the specific impulse (Isp) and density impulse (ρIsp). The use of HMOFs to produce paraffin-based hypergolic fuels results in a slight decrease of the Isp and ρIsp compared to that of pure paraffin, similar to the effect observed with Ammonia Borane (AB), a popular hypergolic additive. HMOFs however have a much higher thermal stability, allowing for convenient mixing with hot liquid paraffin, making the manufacturing processes simpler and safer compared to other hypergolic additives such as AB.
Naive Bayes classification model for isotopologue detection in LC-HRMS data
Authors: van Herwerden Denice , O'Brien Jake , Choi Phil , Thomas Kevin , Schoenmakers Peter , Samanipour Saer
Published: February 2022

Isotopologue identification or removal is a necessary step to reduce the number of features that need to be identified in samples analyzed with non-targeted analysis. Currently available approaches rely on either predicted isotopic patterns or an arbitrary mass tolerance, requiring information on the molecular formula or instrumental error, respectively. Therefore, a Naive Bayes isotopologue classification model was developed that does not depend on any thresholds or molecular formula information. This classification model uses elemental mass defects of six elemental ratios and can successfully identify isotopologues in both theoretical isotopic patterns and wastewater influent samples, outperforming one of the most commonly used approaches (i.e., 1.0033 Da mass difference method - CAMERA).
Addressing Missing Data in Untargeted Metabolomics: Identifying Missingness Type and Evaluating the Impact of Imputation Methods on Experimental Replication
Authors: Davis Trenton J. , Firzli Tarek R. , Higgins Keppler Emily A. , Richardson Matt , Bean Heather D.
Published: February 2022

Missing data is a significant issue in metabolomics that is often neglected when conducting data pre-processing, particularly when it comes to imputation. This can have serious implications for downstream statistical analyses and lead to misleading or uninterpretable inferences. In this study, we aim to identify the primary types of missingness that affect untargeted metabolomics data and compare strategies for imputation using two real-world comprehensive two-dimensional gas chromatog-raphy (GC×GC) data sets. We also present these goals in the context of experimental replication whereby imputation is conducted in a within-replicate-based fashion—the first description and evaluation of this strategy—and introduce an R package MetabImpute to carry out these analyses. Our results conclude that, in these two data sets, missingness was most likely of the missing at-random (MAR) and missing not-at-random (MNAR) types as opposed to missing completely at-random (MCAR). Gibbs sampler imputation and Random Forest gave the best results when imputing MAR and MNAR compared against single-value imputation (zero, minimum, mean, median, and half-minimum) and other more sophisticated approach-es (Bayesian principal components analysis and quantile regression imputation for left-censored data). When samples are replicated, within-replicate imputation approaches led to an increase in the reproducibility of peak quantification compared to imputation that ignores replication, suggesting that imputing with respect to replication may preserve potentially important features in downstream analyses for biomarker discovery.
E2EDNA: Simulation Protocol for DNA Aptamers with Ligands
Authors: Kilgour Michael , Liu Tao , Walker Brandon , Ren Pengyu , Simine Lena
Published: February 2022

We present E2EDNA, a simulation protocol and accompanying code for the molecular biophysics and materials science communities. This protocol is both easy to use and sufficiently efficient to simulate single-stranded (ss)DNA and small analyte systems that are central to cellular processes and nanotechnologies such as DNA aptamer-based sensors. Practical aptamer optimization often requires higher accuracy predictions for only a small subset of sequences suggested e.g., by SELEX experiments, but in the absence of a streamlined procedure this task is extremely time and expertise intensive. We address this gap by introducing E2EDNA, a computational framework that accepts a DNA sequence in the FASTA format and the structures of the desired ligands, and performs approximate folding followed by a refining step, analyte complexation, and molecular dynamics sampling at the desired level of accuracy. As a case study we simulate a DNA-UTP (uridine triphosphate) complex in water using AMOEBA force field. https://github.com/InfluenceFunctional/E2EDNA.
Design of Long-Term Stable Concentrated Colloidal Dispersions in Ionic Liquids up to 473 K
Authors: Riedl Jesse Cornelius , Sarkar Mitradeep , Fiuza Thiago , Cousin Fabrice , Depeyrot Jérome , DUBOIS Emmanuelle , Mériguet Guillaume , Perzynski Régine , Peyre Véronique
Published: February 2022

Some of the most promising fields of application of ionic liquid-based colloids imply elevated temperatures. Their careful design and analysis is therefore essential. The system studied are iron oxide nanoparticles (NPs) dispersed in ethyl-methylimidazolium bistriflimide (EMIM TFSI). The key parameters of the solid-liquid interface, tuned at room temperature, are the surface charge density and the nature of the counterions. The thermal stability of these nanoparticle dispersions is then analysed on the short and long term up to 473 K. A multiscale analysis is performed combining dynamic light scattering (DLS), small angle X-ray/neutron scattering (SAXS/SANS) and thermogravimetric analysis (TGA). With a careful choice of the species at the solid-liquid interface, ionic liquid-based colloidal dispersions of iron oxide NPs in EMIM TFSI stable over years at room temperature can be obtained, also stable at least over days up to 473 K and NPs concentrations up to 12 vol% (30 wt%).
Synthetic Studies on the Indane SHIP1 Agonist AQX-1125.
Authors: Dungan Otto , Dormann Shawn , Fernandes-Denney Sandra , Duffy Brian , Effiong Daniel , Kerr William , Chisholm John
Published: February 2022

A new synthetic route to the SHIP1 agonist AQX-1125 has been developed. This sequence utilizes a hydroxy-acid intermediate which allows for ready differentiation of the C6 and C7 positions. The role of the C17 alkene in the biological activity of the system is also investigated, and this functional group is not required for SHIP1 agonist activity.