bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of nanoparticles with lipid films: the role of symmetry
Authors: Caselli Lucrezia , Ridolfi Andrea , Mangiapia Gaetano , Maltoni Pierfrancesco , Moulin Jean-Francois , Berti Debora , Steinke Nina-Juliane , Gustafsson Emil , Nylander Tommy , Montis Costanza
Published: February 2022

When nanomaterials are put in contact with living organisms, their interaction with biomacromolacules and biological barriers will determine their bioactivity, biological fate and cytotoxicity. In this context, the role of symmetry/shape anisotropy of both the nanomaterials and the biological interfaces on their interaction mechanism, is a relatively unaddressed issue. Here, we study the interaction of gold nanoparticles (NPs) of different shape (nanospheres and nanorods) with biomimetic membranes of different symmetry, i.e. flat membranes (of 2D symmetry, representative of the most common plasma membrane geometry), and cubic membranes (of 3D symmetry, representative of non-lamellar membranes, encountered in Nature in peculiar biological conditions). Through an ensemble of structural techniques (Neutron Reflectometry, Grazing Incidence Small-Angle Neutron Scattering), we found that, on a nanometric lengthscale, the structural stability of the membrane towards NPs is dependent on the topological characteristic of the lipid assembly and of the NPs, with higher symmetry related to higher stability. In addition, Confocal Laser Scanning Microscopy analyses highlight, on a micrometric legthscale, that cubic and lamellar phases interact with NPs according to two distinct mechanisms, related to the different structures of the lipid assemblies. This study represents a first attempt to systematically study the role of membrane symmetry on the interaction with NPs; the results will contribute to improve the fundamental knowledge on nano-bio interfaces and, more in general, will provide new insights on the biological function of non-lamellar cubic arrangements of interfacial membranes as a response strategy.
Synergetic effect of metal-organic framework UiO-66 and silver plasmonic nanoparticles on PET waste support in degradation of nerve agent simulant
Authors: Semyonov Oleg , Kogolev Dmitry , Trelin Andrii , Yusubov Mekhman , Guselnikova Olga , Postnikov Pavel
Published: February 2022

The combination of versatile metal-organic frameworks (MOFs) with high porosity and catalytic activity with plasmonic nanoparticles (PNPs) defines a new paradigm in photocatalytic degradation of ecotoxicants. Herein, we prepared a novel composite from a waste polyethylene terephthalate, MOF – UiO-66 and silver nanoparticles (AgNPs) for degradation of nerve agent simulant paraoxon-ethyl, where the additional plasmon excitation at 455 nm enhances Lewis’s acid activity of UiO-66. The obtained material was characterized by spectroscopic: XRD, UV-Vis, FT-IR, XPS, microscopic: SEM, TEM and ICP-MS and TGA. We found the balance between pore availability of UiO-66 for paraoxon-ethyl adsorption to Lewis sites, plasmonic enhancement, and cost minimization in optimal material through variation of added Ag precursor amounts PET@UiO-66-Ag25. Synergetic mechanisms enhanced the degradation rate by more than 3 times compared to PET@UiO-66 with the quantitative paraoxon degradation for 1 hour (>95 %) and >99 % for 2 hours. Moreover, the prepared material is overperforming other materials in terms of environmental impact, easiness of preparation, visible light usage, high apparent quantum yield and recycling performance.
Self-supervised molecular pretraining strategy for reaction prediction in low-resource scenarios
Authors: Zhang Chengyun , Cai Xiang , Qiao Haoran , Zhang Yun , Wu Yejian , Wang Xinqiao , Xie Haiying , Luo Feng , Duan Hongliang
Published: February 2022

In the face of low-resource reaction training samples, we construct a chemical platform for addressing small-scale reaction prediction problem. By using a self-supervised molecular pretraining strategy, the chemical information from 1 billion molecules can be delivered to small-scale reaction prediction. To demonstrate the broad applicability of our approach, we apply our model to three different name reaction prediction tasks. In the Baeyer-Villiger, Heck and Sharpless asymmetric epoxidation reactions, the accuracies increase by 5.7%, 10.8%, 4.8% on average, respectively.
Self-supervised molecular pretraining strategy for low-resource reaction prediction scenarios
Authors: Zhang Chengyun , Cai Xiang , Qiao Haoran , Zhang Yun , Wu Yejian , Wang Xinqiao , Xie Haiying , Luo Feng , Duan Hongliang
Published: February 2022

In the face of low-resource reaction training samples, we construct a chemical platform for addressing small-scale reaction prediction problem. By using a self-supervised pretraining strategy called MASS, the transformer model can absorb the chemical information about 1 billion molecules and then finetunes on small-scale reaction prediction, which is different from previous works that only rely on reaction samples. To demonstrate the broad applicability of our approach, we adopt three dif-ferent name reactions in our work. In the Baeyer-Villiger, Heck and Sharpless asymmetric epoxidation reaction prediction tasks, the average accuracies increase by 5.7%, 10.8%, 4.8% respectively, marking an important step to low-resource reaction prediction.
Photocatalytic reduction of nicotinamide co-factor by perylene sensitized Rh(III) complexes
Authors: Brückmann Jannik , Müller Carolin , Friedländer Ilse , Mengele Alexander , Peneva Kalina , Rau Sven , Dietzek-Ivanšić Benjamin
Published: February 2022

We report a catalytically active intramolecular photocatalyst, which combines a perylene photosensitizer and a Rh(III) catalyst. Spectroscopic studies reveal the formation of a charge-separated perylene radical cation-Rh(II) intermediate that results in a catalytically active species in the presence of protons.
An Efficient GaMD Multi-Level Enhanced Sampling Strategy for Polarizable Force Fields Simulations of Large Biological Systems
Authors: Célerse Fréderic , Jaffrelot-Inizan Theo , Lagardère Louis , Adjoua Olivier , Monmarché Pierre , Mia Yinglong , Derat Etienne , Piquemal Jean-Philip
Published: February 2022

We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs -accelerated implementation within Tinker-HP. For the specific use with the flexible AMOEBA polarizable force field (PFF), we introduce the new "dual–water" GaMD mode. By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups with fast multiple–timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual–water approach is tested on the 1D Potential of Mean Force (PMF) of the CD2–CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS–GaMD capabilities but also the introduction of the new Adaptive Sampling–US–GaMD (ASUS–GaMD) scheme. The highly parallel ASUS–GaMD setup decreases time to convergence by respectively 10 and 20 compared to GaMD–US and US.
Learning H-Coupled 13C NMR in the First Month of Sophomore Organic Lecture
Authors: Taber Douglass
Published: February 2022

Using 13C NMR data that includes 1H coupling allows sophomore organic students to solve simple structural problems, even early in the first semester of the sophomore organic course.
Structural and Data Science-Driven Analysis to Assess Substrate Specificity of Diketopiperazine Reverse Prenyltransferase NotF: Cascade Biocatalytic Synthesis of (–)-Eurotiumin A
Authors: Kelly Samantha P. , Shende Vikram V. , Flynn Autumn R. , Dan Qingyun , Ye Ying , Smith Janet L. , Tsukamoto Sachiko , Sigman Matthew S. , Sherman David H.
Published: February 2022

Prenyltransfer is an early-stage carbon–hydrogen bond (C–H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Towards the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). In the biosynthesis of cytotoxic notoamide metabolites, PT NotF is responsible for catalyzing the first tailoring event of C2 reverse prenyltransfer of brevianamide F (cyclo(L-Trp-L-Pro)). Obtaining a high-resolution crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent exposed substrate binding site, intimating NotF may possess significant substrate promiscuity. To assess the full potential of NotF’s broad substrate selectivity, we synthesized a panel of 30 tryptophanyl DKPs with a suite of sterically and electronically differentiated amino acids, which were selectively prenylated by NotF in often synthetically useful conversions (2 to >99%). Quantitative representation of this substrate library enabled the development of a descriptive statistical model that provided insight into the origins of NotF’s substrate promiscuity. Through this unique approach for understanding enzyme scope, we identified key substrate descriptors such as electrophilicity, size, and flexibility, that govern enzymatic turnover by NotF. Additionally, we demonstrated the ability to couple NotF-catalyzed prenyltransfer with oxidative cyclization using recently characterized flavin monooxygenase, BvnB, from the brevianamide biosynthetic pathway. This one-pot, in vitro biocatalytic cascade proceeds with exceptional substrate recognition, and enabled the first chemoenzymatic synthesis of the marine fungal natural product, (–)-eurotiumin A, in three steps and 60% overall yield.
Biomimetic Brønsted Acid-Catalyzed Carbonyl-Olefin Metathesis Enabled by Hydrogen Bonding Networks
Authors: To Tuong Anh , Pei Chao , Koenigs Rene , Nguyen Thanh Vinh
Published: February 2022

Synthetic chemists have learned to mimic nature in using hydrogen bonds and other weak interactions to dictate the spatial arrangement of reaction substrates and to stabilize transition states to enable highly efficient and selective reactions. The activation of a catalyst molecule itself by hydrogen bonding networks, in order to control its catalytic activity to achieve desired reaction outcomes is much less explored in organic synthesis, despite being a common strategy in nature. Herein, we show our investigation into this underexplored area by studying the promotion of carbonyl-olefin metathesis reactions by hydrogen bonding-assisted Brønsted acid catalysis. The carbonyl-olefin metathesis reaction has recently emerged as a powerful synthetic tool for functional group interconversion of carbonyls and alkenes. However, the application of Brønsted acid catalysts in carbonyl-olefin metathesis reaction, especially in homogeneous conditions, remains scarce and poorly understood. In this work, we report the use of hexafluoroisopropanol solvent in combination with para-toluenesulfonic acid to efficiently catalyze carbonyl-olefin metathesis reactions. Our experimental and computational mechanistic studies reveal not only an interesting role of HFIP solvent in assisting this Brønsted acid catalyzed reaction but also insightful knowledge about the current limitations of the carbonyl-olefin metathesis reaction.
Large, tunable and reversible pH changes by spiropyran photoacids
Authors: Wimberger Laura , Prasad Shyamal , Andréasson Joakim , Schmidt Timothy , Beves Jonathon
Published: February 2022

Molecular photoswitches capable of generating pH changes with precision will allow pH-dependent processes to be controlled remotely and non-invasively with light. We introduce a series of new spiropyran photoswitches, delivering reversible bulk pH changes up to 3.2 pH units (pH 6.5 to pH 3.3) upon irradiation with 450 nm light, displaying tunable and predictable timescales for thermal recovery. We present models to show that the key parameters for optimizing the bulk pH changes are measurable: the solubility of the photoswitch, the acidity of the merocyanine form influenced by the thermal equilibrium position between the spiropyran and the merocyanine isomers, and the increased acidity under visible light irradiation. Using ultrafast transient absorption spectroscopy, we determine quantum yields for the ring closing reaction and observe the lifetime of the transient cis-merocyanine isomer ranging from 30 to 550 ns. Quantum yields did not appear to be a limitation of bulk pH switching. The models we present use experimentally determined parameters and are, in principle, able to predict the change in pH obtained for any related spiropyran photoacid.
Thermal aging of heteroatom substituted Keggin type aluminum oxo polycation solutions: Aggregation behavior and impacts on dissolved organic carbon and turbidity removal
Authors: Shohel Mohammad , Smith Jack A. , Carolan Margaret A. , Forbes Tori Z.
Published: February 2022

Coagulation processes within water treatment plays an important role in contaminant removal and aluminum-oxo Keggin polycations are proved to be an effective coagulating agents. Previous work demonstrated that heteroatom substitution within the Keggin-type polycation ε-Al13 to form ε-GaAl12 and ε-GeAl12 can enhance removal of bacteria, DOC, and turbidity from wastewater. Additional hydrolysis of the ε-Al13 species to form larger Al30 species has also been shown to improve coagulation, but this aspect has not been evaluated for the ε-GaAl12 and ε-GeAl12 systems. In the current study, hydrolysis of ε-Al13, ε-GaAl12 and ε-GeAl12 was promoted through hydrothermal aging to evaluate the overall solution stability/behavior and water treatment efficiency. Turbidity measurement of aged solution indicated that Ga substituted aluminum-oxo Keggin polycations remain stable in solution and DLS studies demonstrated greater diversity in particle sizes within the system. Additional thermogravimetric analyses of metal hydroxide precipitates formed from the aging studies indicate that the GaAl12 system behaves more like an amorphous Al(OH)3 phase, which has higher solubility than other aluminum hydroxide phases. Hydrothermal aging did not significantly change %DOC removal as all solution showed high efficiency for removal across a range of pH values. GaAl12 solutions demonstrated good turbidity removal efficiency in all pH range, with enhanced performance at pH 5. The study suggests that larger, relatively stable oligomers do exist within the aged GaAl12 solutions that may contribute to enhanced contaminant removal in a similar manner to what is observed within the PACl-Al30 coagulant.
Performance comparison of r2SCAN and SCAN metaGGA density functionals for solid materials via an automated, high-throughput computational workflow
Authors: Kingsbury Ryan , Gupta Ayush , Bartel Christopher , Munro Jason , Dwaraknath Shyam , Horton Matthew , Persson Kristin
Published: February 2022

Computational materials discovery efforts utilize hundreds or thousands of density functional theory (DFT) calculations to predict material properties. Historically, such efforts have performed calculations at the generalized gradient approximation (GGA) level of theory due to its efficient compromise between accuracy and computational reliability. However, high-throughput calculations at the higher metaGGA level of theory are becoming feasible. The Strongly Constrainted and Appropriately Normed (SCAN) metaGGA functional offers superior accuracy to GGA across much of chemical space, making it appealing as a general-purpose metaGGA functional, but it suffers from numerical instabilities that impede it's use in high-throughput workflows. The recently-developed r2SCAN metaGGA functional promises accuracy similar to SCAN in addition to more robust numerical performance. However, its performance compared to SCAN has yet to be evaluated over a large group of solid materials. In this work, we compared r2SCAN and SCAN predictions for key properties of approximately 6,000 solid materials using a newly-developed high-throughput computational workflow. We find that r2SCAN predicts formation energies more accurately than SCAN and PBEsol for both strongly- and weakly-bound materials and that r2SCAN predicts systematically larger lattice constants than SCAN. We also find that r2SCAN requires modestly fewer computational resources than SCAN and offers significantly more reliable convergence. Thus, our large-scale benchmark confirms that r2SCAN has delivered on its promises of numerical efficiency and accuracy, making it a preferred choice for high-throughput metaGGA calculations.
Near-infrared-active upconverting niobium-doped black titanium dioxide photocatalysts
Authors: Nganou Collins , Carrier Andrew , Shafiee Ali , Yu Naizhen , Oakes Ken , Zhang Xu
Published: February 2022

Black titanium dioxide is a broadband-absorbing photocatalyst characterized by integration of atomic hydrogen within the outer layers of anatase nanomaterials. In addition to is broad absorbance of visible to near-infrared light, the material has some intrinsic upconversion ability, which is greatly enhanced by the addition of a niobium oxide shell. This yields a highly active photocatalyst as demonstrated in photodegradation experiments.
Classifying Natural Products from Plants, Fungi or Bacteria using the COCONUT Database and Machine Learning
Authors: Capecchi Alice , Reymond Jean-Louis
Published: February 2022

Natural products (NPs) represent one of the most important resources for discovering new drugs. Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the recently reported Collection of Open Natural Products (COCONUT) database assigned to plants, fungi, or bacteria. Visualizing this subset in an interactive tree-map (TMAP) calculated using MAP4 (MinHashed atom pair fingerprint) clustered NPs according to their assigned origin (https://tm.gdb.tools/map4/coconut_tmap/), and a support vector machine (SVM) trained with MAP4 correctly assigned the origin for 94% of plant, 89% of fungal, and 89% of bacterial NPs in this subset. An online tool based on an SVM trained with the entire subset correctly assigned the origin of further NPs with similar performance (https://np-svm-map4.gdb.tools/). Origin information might be useful when searching for biosynthetic genes of NPs isolated from plants but produced by endophytic microorganisms.
Towards reliable three-electrode cells for lithium–sulfur batteries
Authors: Chien Yu-Chuan , Brandell Daniel , Lacey Matthew J.
Published: February 2022

Three-electrode measurements are valuable to the understanding of the electrochemical processes in a battery system. However, their application in lithium–sulfur chemistry is difficult due to the complexity of the system and thus rarely reported. Here, we present a simple three-electrode cell format with relatively good life time and minimum interference with the cell operation.
Results of VAMAS Survey Regarding Microplastic Issues
Authors: Federici Stefania , Rani Monika , Depero Laura Eleonora
Published: February 2022

Trillions of tiny particles generated by our plastic-reliant society are polluting environments worldwide. An explosion of research has been devoted in the last years to detect, identify and quantify the microplastics, hidden not only in the oceans but also in the world’s rivers, lakes, air, soil as well as food and organisms. Thus, we urgently need reliable standards to support the decision-maker to handle many issues related to this question. In this paper, the results of a VAMAS survey that involved 390 experts are presented and discussed. The inter-laboratory studies urgently needed in the next future are proposed.
Development and Molecular Understanding of a Pd-catalyzed Cyanation of Aryl Boronic Acids Enabled by High-Throughput Experimentation and Data Analysis
Authors: De Jesus Silva Jordan , Bartalucci Niccolò , Jelier Benson , Grosslight Samantha , Gensch Tobias , Schünemann Claas , Müller Bernd , Kamer Paul C. J. , Copéret Christophe , Sigman Matthew S. , Togni Antonio
Published: February 2022

A synthetic method for the palladium-catalyzed cyanation of aryl boronic acids using bench stable and non-toxic N-cyanosuccinimide has been developed. High-throughput experimentation facilitated the screen of 90 different ligands and the resultant statistical data analysis identified that ligand σ–donation, π–acidity and sterics are key drivers that govern yield. Categorization into three ligand groups – monophosphines, bisphosphines and miscellaneous – was performed before the analysis. For the monophosphines, the yield of the reaction increases for strong σ–donating, weak π–accepting ligands, with flexible pendant substituents. For the bisphosphines, the yield predominantly correlates with ligand lability. The applicability of the designed reaction to a wider substrate scope was investigated, showing good functional group tolerance in particular with boronic acids bearing electron-withdrawing substituents. This work outlines the develop-ment of a novel reaction, coupled with a fast and efficient workflow to gain understanding of the optimal ligand properties for the design of improved palladium cross-coupling catalysts.
[Fe15]: A Frustrated, Centred Tetrakis Hexahedron
Authors: Cutler Daniel , Singh Mukesh , Nichol Gary , Evangelisti Marco , Schnack Juergen , Cronin Leroy , Brechin Euan
Published: February 2022

The combination of two different FeIII salts in a solvothermal reaction with triethanolamine results in the formation of a high symmetry [FeIII15] cluster whose structure conforms to a centred, tetrakis hexahedron.
Multi-State Density Functional Theory for Ground and Excited States
Authors: Lu Yangyi , Gao Jiali
Published: February 2022

We report a rigorous formulation of multi-state density functional theory (MSDFT) that extends the Kohn-Sham (KS) energy functional for the ground state to a Hamiltonian matrix functional H[D] of the density matrix D in the space spanned by the lowest N adiabatic states. We establish a variational principle of MSDFT, which guarantees that the variational optimization results in a Hamiltonian matrix, whose eigenvalues are the lowest N eigen-energies of the system. We present an explicit expression of H[D] and introduce the correlation matrix functional. Akin to KS-DFT for the ground state, a universal multi-state correlation potential is derived for a two-state system as an illustrative example. This work shows that MSDFT is an exact density functional theory that treats the ground and excited states on an equal footing and provides a framework for practical applications and future developments of approximate functionals for excited states.
Raman Tweezers for Tire and Road Wear Micro- and Nanoparticles analysis
Authors: Raymond Gillibert , Magazzù Alessandro , Callegari Agnese , Brente Ciriza David , Antonino Foti , Donato Maria Grazia , Maragò Onofrio M. , Volpe Giovanni , Lamy de La Chapelle Marc , Lagarde Fabienne , Gucciardi Pietro Giuseppe
Published: February 2022

Tire and Road Wear Particles (TRWP) are non-exhaust particulate matter generated by road transport means during the mechanical abrasion of tires, brakes and roads. TRWP accumulate on the roadsides and are transported into the aquatic ecosystem during stormwater runoffs. Due to their size (sub-millimetric) and rubber content (elastomers), TRWP are considered microplastics (MPs). While the amount of the MPs polluting the water ecosystem with sizes from ~ 5 μm to more than 100 μm is known, the fraction of smaller particles is unknown due to the technological gap in the detection and analysis of < 5 μm MPs. Here we show that Raman Tweezers, a combination of optical tweezers and Raman spectroscopy, can be used to trap and chemically analyze individual TWRPs in a liquid environment, down to the sub-micrometric scale. Using tire particles mechanically grinded from aged car tires in water solutions, we show that it is possible to optically trap individual sub-micron particles, in a so-called 2D trapping configuration, and acquire their Raman spectrum in few tens of seconds. The analysis is then extended to samples collected from a brake test platform, where we highlight the presence of sub-micrometric agglomerates of rubber and brake debris, thanks to the presence of additional spectral features other than carbon. Our results show the potential of Raman Tweezers in environmental pollution analysis and highlight the formation of nanosized TRWP during wear.
Bias corrections for speciated and source-resolved PM2.5 chemical transport model simulations using a geographically weighted regression
Authors: Hernandez Carlos , Skyllakou Ksakousti , Garcia Rivera Pablo , Dinkelacker Brian , Marshall Julian , Pope Arden , Robinson Allen , Pandis Spyros , Adams Peter
Published: February 2022

The ability to provide speciated and source-resolved PM2.5 estimates make chemical transport models a potentially valuable tool for exposure assessments. However, epidemiological studies often require unbiased estimates, which can be challenging for chemical transport models. We use geographically weighted regression to predict and correct the bias in source-resolved PM2.5 species (elemental carbon, organic aerosol, ammonium, nitrate, and sulfate) across the continental U.S. for 2001 and 2010. The regression models are trained using speciated ground-level monitors from the CSN and IMPROVE networks. A 10-fold cross-validation shows minimal bias across all simulated PM2.5 species (0 – 3%) and improved agreement with ground-level monitors (R2 = 0.53 – 0.97). Corrections also improve the agreement between simulated and observed species mixtures on a fractional basis. The source-resolved exposure estimates developed in this study are suitable for use in health analyses of PM2.5 toxicity.
A Bioinspired Threonine-based Antifreeze Protein Mimic with Potent Ice Recrystallization Inhibition Activity
Authors: Delesky Elizabeth , Garcia Luis , Lobo Aparna , Wallat Jaqueline , Miyake Garret , Srubar III Wil
Published: February 2022

Ice growth mitigation is a pervasive challenge for multiple industries. In nature, ice-binding proteins (IBPs) demonstrate potent ice-growth prevention through ice recrystallization inhibition (IRI). However, IBPs are expensive, difficult to produce in large quantities, and exhibit minimal resilience to non-physiological environmental stressors, such as elevated pH. For these reasons, researchers have turned to polymeric bioinspired mimics. To-date, however, no mimic has rivaled the ability of native IBPs to display IRI activity at ultra-low nanomolar concentrations. In this work, we study the IRI activity of peptides and polypeptides inspired by common ice-binding residues of IBPs to inform the synthesis and characterization of a potent bioinspired polymer mimic. We show first that the threonine polypeptide (pThr) displays the best IRI activity in phosphate-buffered saline (PBS). Second, we use pThr as a molecular model to synthesize and test a new bioinspired polymer mimic, poly(2-hydroxypropyl methacrylamide) (pHPMA). We show that pHPMA exhibits potent IRI activity in neutral PBS at nanomolar concentrations. These results substantiate that pHPMA outperforms poly(vinyl alcohol) (PVA), the current top performing IBP mimic in the field, in terms of effectiveness at mitigating ice crystal growth at concentrations akin to native IBPs.
A fluorescent amyloid sensor for quantitative super-resolution imaging of amyloid fibril assembly.
Authors: Kaur Amandeep , Adair Liam D. , Ball Sarah R. , New Elizabeth J. , Sunde Margaret
Published: February 2022

Many soluble proteins can self-assemble into macromolecular structures called amyloids, a subset of which are implicated in a range of neurodegenerative disorders. The nanoscale size and structural heterogeneity of prefibrillar and early aggregates, as well as mature amyloid fibrils, pose significant challenges for the quantification of amyloid species, identification of their cellular interaction partners and for elucidation of the molecular basis for cytotoxicity. We report a fluorescent amyloid sensor AmyBlink-1 and its application in super-resolution imaging of amyloid structures. AmyBlink-1 exhibits a 5-fold increase in ratio of the green (thioflavin T) to red (Alexa Fluor 647) emission intensities upon interaction with amyloid fibrils. Using AmyBlink-1, we performed nanoscale imaging of four different types of amyloid fibrils, achieving a resolution of ~30 nm. AmyBlink-1 enables molecular-level visualization and subsequent quantification of morphological features, such as the length and skew of individual amyloid aggregates formed at different times along the amyloid assembly pathway.
Antibacterial Activity of the Root Extracts of Garcinia Kola Against MDR Staphylococcus Aureus : Invitro and Insilico Studies
Authors: Haliru Yakubu Abdulbasit , Mustapha Muhammad Muhammad
Published: February 2022

Multi-Drug Resistant (MDR) Staphylococcus aureus is an important bacteria with clinical and economic implications. Plants including Garcinia kola provides bioactive principles with diverse structural and biological features. Tyrosyl-tRNA synthetase (TyrRS) is targeted in antibacterial drug discovery as its implicated in bacterial protein synthesis. The n-Butanol fraction of Garcinia kola root extract recorded the highest activity against MDR staph aureus (18.50±0.41) compared to the chloroform (10.00±2.12) and methanol (8.16±0.62) extract, with no activity recorded with the n-Hexane extract. Analysis of the n-Butanol fraction on GC-MS recorded 14 phytoconstituents with varying structural composition; containing important scaffolds & motifs of benzoquinone, imidazole[1,2-a]pyridine, chlorocarbazole and azetidine that present key pharmaceuticals as antibiotic and for drug development. Further insilico molecular docking studies of these compounds on antibacterial drug target; Tyrosyl-tRNA synthetase (PDB 1JIJ) from MDR staph aureus were documented. Nine (9) compounds had good binding scores ranging from -4.63 to -7.08 kcal/mol; with CID_590350 having the highest score. The compounds formed various bonding with the 1JIJ amino acid residues including H-bond, van der waal and π interactions. Five (5) compounds; CID_619583 (9,9-Dichloro-9-silafluorene), CID_5732 (Zolpidem), CID_616643 (Pyridazine-3,5-dicarbonitrile, 1,6-dihydro-4-amino-6-imino-1-(2-nitrophenyl)), CID_16486 ((S)-(-)-2-Azetidinecarboxlic acid) and CID_66747 (2-Hydroxyethyl benzoate) showed favorable ADME properties, while their MD stimulation analysis revealed stable binding capabilities with the drug target. CID_16486 and CID_66747 bind to the most active binding pocket (Drug score: 0.82 and 0.72) while CID_619583 tends to bind outside the active binding pocket. Therefore, these compounds from the root of Garcinia kola are considered as suitable prospective bioactive compounds against MDR Staphylococcus aureus after successful in vitro and in silico experimental validation.
The Phospha-Bora-Wittig Reaction
Authors: Borys Andryj , Rice Ella , Nichol Gary , Cowley Michael
Published: February 2022

We report the phospha-bora-Wittig reaction for the direct preparation of phosphaalkenes from aldehydes, ketones, esters, or amides. The transient phosphaborene Mes*P=B-NR2 reacts with carbonyl compounds to form 1,2,3-phosphaboraoxetanes, analogues of oxaphosphetane intermediates in the classical Wittig reaction. 1,2,3-phosphaboraoxetanes undergo thermal or Lewis acid-promoted cycloreversion, yielding phosphaalkenes. Experimental and density functional theory studies reveal far-reaching similarities between classical and phospha-bora-Wittig reactions.
Sustainable nitrate production out of thin air: The photocatalytic oxidation of molecular nitrogen
Authors: Pashkova Aneta , Burek Bastien , Bloh Jonathan
Published: February 2022

Novel processes for the sustainable production of fertilizers are highly sought after to combat climate change. Herein, we demonstrate that by irradiating with strong UVA-light, TiO2 is able to photocatalytically oxidize molecular nitrogen in the gas phase under ambient conditions to NOx and nitrate. The reaction produces predominantly nitrogen dioxide with a high selectivity of up to 93% which could be captured afterwards to produce nitric acid or nitrates and used as sustainable (solar) fertilizer.
Synthesis of 1-(1-Arylvinyl)pyridin-2(1H)-ones from Ketones and 2-Fluoropyridine
Authors: Kawamoto Takuji , Ikeda Shunya , Kamimura Akio
Published: February 2022

Pyridone skeletons are found in numerous biologically active molecules and pharmaceuticals. 1-(1-Arylvinyl)pyridin-2(1H)-ones are synthetic intermediates derived from the enamide moiety, and only few examples of the synthesis of 1-(1-arylvinyl)-2-pyridones have been reported. In this work, a simple and efficient procedure for the synthesis of N-vinyl-substituted pyridones from ketones and 2-fluoropyridine in the presence of trifluoromethane sulfonic anhydride, followed by base treatment is described. Various ketones with electron-donating or -withdrawing groups at the benzene rings can be used in this reaction. A preliminary mechanistic study indicates that it is not very likely that both vinyl triflates and vinyl cations play major roles as intermediates in this transformation. The thus obtained pyridones can be subsequently transformed via C–H arylation and radical alkylation reactions.
How Globally Aromatic Are Six-Porphyrin Nanorings?
Authors: Deng Jie-Ren , Bradley David , Jirásek Michael , Anderson Harry , Peeks Martin
Published: February 2022

A recent Research Article published in this journal by Matito and coworkers claimed that none of the oxidation states of a butadiyne-linked six-porphyrin nanoring exhibit global aromaticity or antiaromaticity. Here we show that this conclusion is incorrect. A combination of density functional theory (DFT) calculations and experimental NMR data provides compelling evidence for global (anti)aromaticity in a variety of six-porphyrin nanorings in their 2+, 4+ and 6+ oxidation states. The strength of the predicted ring current depends on the choice of DFT functional, so it is crucial to use a functional that reproduces the experimental 1H NMR chemical shifts in these cations.
Free and Open Source Software for Computational Chemistry Education
Authors: Lehtola Susi , Karttunen Antti
Published: February 2022

Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight-binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. We discuss the availability and use of various FOSS quantum chemistry packages and demonstrate what kinds of calculations are feasible with these programs, assuming only extremely modest computational resources. Our examples confirm that FOSS software enables decentralized approaches to computational chemistry education within the BYOD scheme, affording a democratization of the science of computational chemistry as well.
Free and Open Source Software for Computational Chemistry Education
Authors: Lehtola Susi , Karttunen Antti
Published: February 2022

Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. Our brief review on various free and open source software (FOSS) quantum chemistry packages points out the existence of software offering a wide range of functionality, all the way from approximate semiempirical calculations with tight-binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. Combined with the remarkable increase in the computing power of personal devices, which now rivals that of the fastest supercomputers in the world of the 1990s, we demonstrate that a decentralized model for teaching computational chemistry is now possible thanks to FOSS computational chemistry packages, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device (BYOD) scheme. FOSS software can be made trivially simple to install and keep up to date, eliminating the need for departmental support, and also enables comprehensive teaching strategies, as various algorithms' actual implementations can be used in teaching. We exemplify what kinds of calculations are feasible with four FOSS electronic structure programs, assuming only extremely modest computational resources, to illustrate how FOSS packages enable decentralized approaches to computational chemistry education within the BYOD scheme. FOSS also has further benefits: the open access to the source code of FOSS packages democratizes the science of computational chemistry, and FOSS packages can be used without limitation also beyond education, in academic and industrial applications, for example. For these reasons, we believe FOSS will become ever more pervasive in computational chemistry.
Antagonistic Role of Aqueous Complexation in the Solvent Extraction and Separation of Rare Earth Ions
Authors: Sun Pan , Binter Erik A. , Liang Zhu , Brown M. Alex , Gelis Artem V. , Benjamin Ilan , Bera Mrinal K. , Lin Binhua , Bu Wei , Schlossman Mark L.
Published: February 2022

During solvent extraction of rare earth ions, an aqueous electrolyte solution is placed in contact with an immiscible organic solution of extractants to enable extractant-facilitated transport of ions into the organic solvent. Although ex-perimental methodologies such as x-ray and neutron scattering have been applied to characterize ion-extractant complexes, identifying the site of ion-extractant complexation has proven challenging. Here, we use tensiometry and surface-sensitive x-ray scattering to study the surface of aqueous solutions of lanthanide chlorides and the water-soluble extractant bis(2-ethylhexyl) phosphate (HDEHP), in the absence of a coexisting organic solvent. These studies restrict interactions of HDEHP with trivalent lanthanide ions to the aqueous phase and the liquid-vapor interface, allowing us to explore the consequences that one or the other is the site of ion-extractant complexation. Unexpectedly, we find that light lanthanides preferentially occupy the liquid-vapor interface, with an overwhelming preference for a light lanthanide, Nd, when present in a mixture with a heavy lanthanide, Er. This contradicts our expectation that heavy lanthanides should have a higher interfacial density since they are preferentially extracted by HDEHP in the presence of an organic phase. These results reveal the antagonistic role played by ion-extractant complexation within the aqueous phase and clarify the potential advantages of water-insoluble extractants that interact with ions primarily at the interface during the process of solvent extraction.
Potential SARS-CoV-2 Nonstructural Protein 15 (NSP15) Inhibitors: Repurposing FDA-Approved Drugs
Authors: Tang Jason , Tsigelny Igor , Greenberg Jerry , Miller Mark , Kouznetsova Valentina
Published: February 2022

Purpose: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths worldwide, pushing the urgent need for an efficient treatment. Nonstructural protein 15 (NSP15) is a promising target due to its importance for SARS-CoV-2’s evasion of the host’s innate immune response. Methods: Using the crystal structure of SARS-CoV-2 NSP15 endoribonuclease, we developed a pharmacophore model of the functional centers in the NSP15 inhibitor’s binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. The conformations of these compounds underwent 3D fingerprint similarity clustering, and possible conformers were docked to the NSP15 binding pocket. We also simulated docking of random compounds to the NSP15 binding pocket for comparison. Results: This search identified 170 compounds as potential inhibitors of SARS-CoV-2 NSP15. The mean free energy of docking for the group of potential inhibitors were significantly lower than for the group of random compounds. Twenty-one of the compounds identified as potential NSP15 inhibitors were antiviral compounds used in the inhibition of a range of viruses, including MERS, SARS-CoV, and even SARS-CoV-2. Eight of the selected antiviral compounds in cluster A are pyrimidine analogues, six of which are currently used in a clinical setting. Four tyrosine kinase inhibitors were identified with potential SARS-CoV-2 inhibition, which is consistent with previous studies showing some kinase inhibitors acting as antiviral drugs. Conclusions: We recommended testing of these 21 selected antiviral compounds for the treatment of COVID-19.
Functionalization of mono- and bimetallic MIL-100(Al,Fe) MOFs by ethylenediamine: post-functionalization, Brønsted acido-basicity and unique CO2 sorption behaviour
Authors: Steenhaut Timothy , Fusaro Luca , Robeyns Koen , Lacour Séraphin , Li Xiao , Mahy Julien G. , Louppe Véronique , Grégoire Nicolas , Barozzino-Consiglio Gabriella , Statsijns Jean-François , Aprile Carmela , Filinchuk Yaroslav , Hermans Sophie
Published: February 2022

The metal sites of MIL-100(Fe), MIL-100(Fe,Al) and MIL-100(Al) MOFs were decorated with ethylenediamine (EN). Interestingly, the Al-containing MOFs presented hierachized porosity, and their structural integrity was maintained upon functionalization. Solution and solid-state NMR confirmed the grafting efficiency in the case of MIL-100(Al) and the presence of a free amine group. It was shown that MIL-100(Al) can be functionalized by only one EN molecule by trimeric Al3O cluster unit, whereas the two other aluminium sites are occupied by an hydroxyl and a water molecule. The -NH2 sites of the grafted ethylenediamine can be used for further post-functionalization through amine chemistry and is responsible for basicity of the functionalized material. Furthermore, the presence of coordinated water molecules on the Al-MOF is responsible for simultaneous Brønsted acidity and for a unique carbon dioxide sorption mecanism, that distinguishes this material from its iron and chromium counterparts.
Scalable and selective β-hydroxy-α-amino acid synthesis catalyzed by promiscuous L-threonine transaldolase ObiH
Authors: Doyon Tyler , Kumar Prasanth , Thien Sierra , Kim Maeve , Stitgen Abigail , Greiger Abbigail , Madigan Cormac , Willoughby Patrick , Buller Andrew
Published: February 2022

Enzymes from secondary metabolic pathways possess broad potential for the selective synthesis of complex bioactive molecules. However, the practical application of these enzymes for organic synthesis is dependent on the development of efficient, economical, operationally-simple and well-characterized systems for preparative scale reactions. We sought to bridge this knowledge gap for the selective biocatalytic synthesis of β-hydroxy-α-amino acids, which are important synthetic building blocks. To achieve this goal, we demonstrated the ability of ObiH, an L-threonine transaldolase, to achieve selective gram-scale synthesis of a diverse array of non-standard amino acids (nsAAs) using a scalable whole cell platform. We show how the initial selectivity of the catalyst is high and how the diastereomeric ratio of products decreases at high conversion due to product re-entry into the catalytic cycle. ObiH-catalyzed reactions with a variety of aromatic, aliphatic and heterocyclic aldehydes selectively generated a panel of β-hydroxy-α-amino acids possessing broad functional-group diversity. Furthermore, we demonstrated that ObiH-generated β-hydroxy-α-amino acids could be modified through additional transformations to access important motifs, such as β-chloro-α-amino acids and substituted α-keto acids.
Multiple C-C bond formation upon electrocatalytic reduction of CO2 by a molecular catalyst
Authors: DONG Si-Thanh , Xu Chen , Lassalle-Kaiser Benedikt
Published: February 2022

Molecular macrocycles show very promising electrocatalytic properties for the reduction of carbon dioxide. Up to now, only C1 products were produced by these catalysts. We show here that iron phthalocyanine, a commercially available molecule based on earth abundant elements, can produce light hydrocarbons upon electrocatalytic reduction of CO2 in aqueous conditions and neutral pH. When an electrochemical potential of -0.7 to -1.1 V vs. RHE is applied to a glassy carbon electrode modified with iron phthalocyanine, carbon monoxide is generated as main product. An increasing fraction of hydrogen is observed as the potential is decreased and small amounts of C1 to C4 saturated and unsaturated products are evolved. Control experiments in the absence of CO2 or catalyst does not produce any of these compounds. X-ray spectroscopic analysis of the electrode during catalysis show that the molecular catalyst remains intact and is responsible from the reaction.
Sustainable Hybrid Route to Renewable Methacrylic Acid via Biomass-Derived Citramalate
Authors: Wu Yuxiao , Shetty Manish , Zhang Kechun , Dauenhauer Paul
Published: February 2022

Combined chemical technologies of microbial fermentation and thermal catalysis provides a hybrid process for sustainable manufacturing of biorenewable sugar-derived monomers for plastics. In this work, methacrylic acid (MAA), a target molecule for the polymer industry, was produced from biomass-derived glucose through the intermediate molecule, citramalic acid. The biosynthetic pathway engineered in E. coli produced citramalic acid intermediate with a high yield (91% of theoretical maximum) from glucose by overexpressing citramalate synthase, removing downstream degradation enzyme 3-isopropylmalate dehydratase, and optimizing the fermentation medium. Thermal heterogeneous catalysis converted the citramalate intermediate to methacrylic acid (MAA) via decarboxylation and dehydration. A selectivity of ~71% for the production of MAA and its intermediate α-hydroxybutyric acid was achieved at a temperature of 250 oC and an acidity of 1.0 mol acid/mol citramalate. An alumina catalyst was found to enhance selectivity to MAA in a single reactor pass from 45.6% in the absence of catalyst to 63.2%. This limited selectivity to MAA was attributed to equilibrium between MAA and α-hydroxybutyric acid, but overall process selectivity to MAA was shown to be higher upon separation and recycle of reaction intermediates. A process flow diagram was proposed of the hybrid route for the conversion of glucose to the final end product, methacrylic acid, for poly(methyl methacrylate) (PMMA).