bluuebunny/crossref_metadata_2025 huggingface dataset:
One-step hydrothermal synthesis of 4-Metylimidazole Decorated Carbon Nanoparticles and Their Fluorescence Enhancement Sensing of Heavy Metal Ions
Authors: Kim Tak , Yun Jung-ho , Boyd Sue , Brown Christopher
Published: February 2022

We report fluorescent carbon nanoparticle decorated with 4-methylimidazole (4-MEI) prepared by a one-step hydrothermal synthesis. Upon binding to toxic heavy metals including Hg2+ and Cd2+, the fluorescence emission displayed notable enhancement. This is in contrast with the majority of other one-step synthesized fluorescent carbon nanoparticle sensing systems which exhibit quenching, due to the non-radiative energy transfer. In comparison, the decorated 4-MEI on the carbon nanoparticles prevents the non-radiative energy transfer when the analytes bind to the 4-MEI. Further results on the fluorescence responses on the removal of the surface decorated 4-MEI and re-coordination of a reference 4-MEI against the same metal ions suggested that the 4-MEI on the carbon nanoparticles’ surface plays a key role in the observed fluorescence enhancement. These features indicate an immense potential for further development of CNP based fluorescence enhancement sensing platforms for effective detection of analytes of interests.
Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis
Authors: Jones Krysten A. , Snodgrass Harrison M. , Belsare Ketaki , Dickinson Bryan C. , Lewis Jared C.
Published: February 2022

Ligand-dependent biosensors are valuable tools for coupling the intracellular concentrations of small molecules to easily detectable readouts such as absorbance, fluorescence, or cell growth. While ligand-dependent biosensors are widely used for monitoring the production of small molecules in engineered cells and for controlling or optimizing biosynthetic pathways, their application to directed evolution for biocatalysts remains underexplored. As a consequence, emerging continuous evolution technologies are rarely applied to biocatalyst evolution. Here, we develop a panel of ligand-dependent biosensors that can detect a range of small molecules. We demonstrate that these biosensors can link enzymatic activity to the production of an essential phage protein to enable biocatalyst-dependent phage assisted continuous evolution (PACE) and phage-assisted continuous selection (PACS). By combining these phage-based evolution and library selection technologies, we demonstrate we can evolve enzyme variants with improved and expanded catalytic properties. Finally, we show that the genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope. These results lay the foundation for using phage-based continuous evolution and selection technologies to engineer biocatalysts with novel substrate scope and reactivity.
One-pot synthesis of oxidation-sensitive supramolecular gels and vesicles
Authors: Duro-Castano Aroa , Rodriguez-Arco Laura , Ruiz-Perez Lorena , De Pace Cesare , Marchello Gabriele , Noble-Jesus Carlos , Battaglia Giuseppe
Published: February 2022

Polypeptide-based nanoparticles offer unique advantages from a nanomedicine perspective such as biocompatibility, biodegradability and stimuli-responsive properties to (patho)physiological conditions. Conventionally, self-assembled polypeptide nanostructures are prepared by first synthesizing their constituent amphiphilic polypeptides followed by post-polymerization self-assembly. Herein, we describe the one-pot synthesis of oxidation-sensitive supramolecular micelles and vesicles. This was achieved by polymerization-induced self-assembly (PISA) of the N-carboxyanhydride (NCA) precursor of methionine using polyethylene oxide as stabilizing and hydrophilic block in dimethyl sulfoxide (DMSO). By adjusting the hydrophobic block length and concentration we obtained a range of morphologies from spherical to worm-like micelles, to vesicles. Remarkably, the secondary structure of polypeptides greatly influenced the final morphology of the assemblies. Surprisingly, worm-like micellar morphologies were obtained for a wide range of methionine block lengths and solid contents, with spherical micelles restricted to very short hydrophobic lengths. Worm-like micelles further assembled into oxidation-sensitive, self-standing gels in the reaction pot. Both vesicles and worm-like micelles obtained using this method demonstrated to degrade under controlled oxidant conditions which would expand their biomedical applications such as in sustained drug release or as cellular scaffolds in tissue engineering.
Facile Synthesis of the Dicyanophosphide Anion via Electrochemical Activation of White Phosphorus: An Avenue to Organophosphorus Compounds
Authors: Mei Yanbo , Yan Zeen , Liu Liu Leo
Published: February 2022

Organophosphorus compounds (OPCs) have gained tremendous interest in the past decades due to their wide applications ranging from synthetic chemistry to materials and biological sciences. We describe herein a practical and versatile approach for the transformation of white phosphorus (P4) into useful OPCs with high P atom economy via a key bridging anion [P(CN)2]–. This anion can be prepared on a gram scale directly from P4 through an unprecedented electrochemical process. A variety of OPCs involving phosphinidenes, cyclophosphanes and phospholides have been made readily accessible from P4 in a two-step manner. Our approach has a significant impact on the future preparation of OPCs in laboratory and industrial settings.
Deep Convolutional Neural Network Algorithm for Prediction of the Mechanical Properties of Friction Stir Welded Copper Joints from its Microstructures
Authors: Mishra Akshansh , Suman Asmita
Published: February 2022

Convolutional Neural Network (CNN) is a special type of Artificial Neural Network which takes input in the form of an image. Like Artificial Neural Network they consist of weights that are estimated during training, neurons (activation functions), and an objective (loss function). CNN is finding various applications in image recognition, semantic segmentation, object detection, and localization. The present work deals with the prediction of the welding efficiency of the Friction Stir Welded joints on the basis of microstructure images by carrying out training on 3000 microstructure images and further testing on 300 microstructure images. The obtained results showed an accuracy of 80 % on the validation dataset.
Using Voltammetry Augmented with Physics-Based Modeling and Bayesian Hypothesis Testing to Estimate Electrolyte Composition
Authors: Fenton, Jr. Alexis , Brushett Fikile
Published: February 2022

Voltammetry is a foundational electrochemical technique that can qualitatively and quantitatively probe electroactive species in electrolytes and as such has been used in numerous fields of study. Recently, automation has been introduced into voltammetric analyses to extend their capabilities (e.g., Bayesian parameter estimation, compound identification via machine learning); however, opportunities exist to enable more versatile methods across a wider range of electrolyte and experimental conditions. Here, we present a protocol that uses experimental voltammetry, physics-driven models, binary hypothesis testing, and Bayesian inference to enable robust labeling of electroactive species in multicomponent electrolytes across multiple techniques. We first describe the development of this protocol, and we subsequently validate the methodology in a case study involving five N-functionalized phenothiazine derivatives. In this analysis, the protocol correctly labeled an electrolyte containing 10H-phenothiazine and 10-methylphenothiazine from both cyclic voltammograms and cyclic square wave voltammograms, demonstrating its ability to identify electroactive constituents of a multicomponent solution. Finally, we identify areas of further improvement (e.g., achieving greater detection accuracy) and future applications to potentially enhance in situ or operando diagnostic workflows.
A non-radioactive mass spectrometry based differential radial capillary action of ligand assay (DRaCALA) to assess ligand binding to proteins
Authors: Cimdins-Ahne Annika , Chernobrovkin Alexey , Zubarev Roman , Römling Ute
Published: February 2022

Binding of ligands to macromolecules changes their physicochemical characteristics. Cyclic di-GMP and other cyclic di-nucleotides are second messengers involved in motility/sessility and acute/chronic infection life style transition. Although the GGDEF domain encoding preferentially a diguanylate cyclase represents one of the most abundant bacterial domain superfamilies, the number of cyclic di-GMP receptors falls short. To facilitate screening for cyclic di-nucleotide binding proteins, we describe a non-radioactive, MALDI-TOF based modification of the widely applied differential radial capillary action of ligand assay (DRaCALA). The results of this assay suggest that YciRFec101, but not the YciRTOB1 variant of the diguanylate cyclase/phosphodiesterase YciR binds cyclic di-GMP.
Electrochemical oscillatory baffled reactors fabricated with additive manufacturing for efficient continuous-flow oxidations
Authors: Alvarez Elena , Romero-Fernandez Maria , Iglesias Diego , Martinez-Cuenca Raul , Okafor Obinna , Delorme Astrid , Lozano Pedro , Goodridge Ruth , Paradisi Francesca , Walsh Darren A. , Sans Víctor
Published: February 2022

Electrochemical oscillatory baffled reactors fabricated with additive manufacturing for efficient continuous-flow oxidations
Electrocatalytic CO2 hydrogenation to C2 based products through C–C coupling over Cu(100) nanocube
Authors: Mandal Shyama Charan , Pathak Biswarup
Published: February 2022

In this study, we have considered a Cu nanocube (Cu-NC) based catalyst exposed with (100) facets for CO2 hydrogenation reactions. All the feasible mechanistic pathways for the formations of C1 (HCOOH, CH3OH and CH4) and C2 (C2H4 and C2H5OH) based products have been explored using the density functional theoretical calculations and the most plausible pathways have been identified. The calculated results are compared with the previous reports on the periodic Cu(100) and Cu(111) surfaces, and also on the surface of Cu85 nanocluster and Cu(111) monolayer. The in-depth mechanistic investigation shows that Cu-NC can be very selective towards the C2 based products with a lower limiting potential (calculated) compared to the periodic surfaces. The underlying reasons for such findings have been explained and compared that with the periodic surfaces. We therefore, propose that the Cu-NC based catalysts can be more promising for C2 based products.
Encoding stereochemical molecular information on cyclophanes using non-directional interactions and achiral building blocks
Authors: Zhang Yuan , Ourri Benjamin , Skowron Pierre-Thomas , Jeamet Emeric , Belenguer Ana , Vanthuyne nicolas , cala olivier , Mandal Pradeep , Duchamp Christian , Dumont Elise , Perret Florent , Vial Laurent , Huc Ivan , Leclaire Julien
Published: February 2022

The stereoselective assembly of achiral constituents through a single spontaneous process into complex covalent architectures bearing multiple stereogenic elements currently seems out of reach to the synthetic chemist. It even seems beyond what nature itself has managed to attain through evolution. Here, we show that such an extreme level of control can be achieved by molecular programming, i.e. by implementing stereo-electronic information on synthetic organic building blocks and exploiting the features of the covalent reactions and interactions, whose interplay acts as a powerful assembling algorithm. Remarkably, we show that non-directional bonds and interactions can reliably transfer this information, delivering in near to physiological conditions, high-molecular weight macrocyclic species carrying up to 8-bits of conformational and configuration information. Beyond the field of supramolecular chemistry, this proof of concept should stimulate the on-demand production of highly structured polyfunctional architectures.
Chemical Design of Self-Propelled Janus Droplets
Authors: Meredith Caleb , Castonguay Alexander , Chiu Yu-Jen , Brooks Allan M. , Moerman Pepijn , Torab Peter , Wong Pak Kin , Sen Ayusman , Velegol Darrell , Zarzar Lauren
Published: February 2022

The study of active colloidal microswimmers with tunable phoretic and self-organizational behaviors is important for understanding out-of-equilibrium systems and the design of functional, adaptive matter. Solubilizing, self-propelling droplets have emerged as a rich chemical platform for exploration of active behaviors, but isotropic droplets rely on spontaneous symmetry breaking to sustain motion. The introduction of permanent asymmetry, e.g. in the form of a biphasic Janus droplet, has not been explored previously as a comprehensive design strategy for active droplets, despite the widespread use of Janus structures in motile solid particles. Here, we uncover the chemomechanical framework underlying the self-propulsion of biphasic Janus oil droplets solubilizing in aqueous surfactant. We elucidate how droplet propulsion is influenced by the degree of oil mixing, droplet shape, and oil solubilization rates for a range of oil combinations. A key finding is that for droplets containing both a mobile (solubilizing) and non-mobile oil, the degree of partitioning of the mobile oil across the Janus droplets’ oil-oil interface plays a pivotal role in determining the droplet speed and swimming direction. In addition, spatiotemporal control over droplet swimming speed and orientation is demonstrated through the application of local thermal gradients applied via joule heating and laser illumination. We also explore the interactions between collections of Janus droplets including the spontaneous formation of multi-droplet clusters that spin predictably based on symmetry. Our findings provide insights as to how the chemistry and structure of multiphase fluids can be harnessed to design microswimmers with programmable active and collective behaviors.
Synthesis of α- and β-Carbolines by a Metalation/Negishi Cross-Coupling/SNAr Reaction Sequence
Authors: Sathiyalingam Shainthavaan , Roesner Stefan
Published: February 2022

Carbolines are considered to be privileged scaffolds in medicinal chemistry. An efficient method for the synthesis of α- and β-carbolines from fluoropyridines and 2-haloanilines is reported. This streamlined procedure consists of a four-step directed ortho-lithiation, zincation, Negishi cross-coupling, and intramolecular nucleophilic aromatic substitution, providing access to a diverse set of functionalized carbolines. While the procedure is applicable to batch conditions, the generation of arylzinc intermediates in continuous flow has been demonstrated.
Polysaccharide - Modified MMT/ Modified MMT/ Polysaccharide – MNP, Lignin - Modified MMT Nanocomposites Verses Polyethyleneimineimine- Modified MMT-: A Comparative Analysis of Sustained Pesticide Delivery
Authors: Mahajan RITU
Published: February 2022

Highlights: • At the nanoscale, the characteristics of a material can alter dramatically. With only a reduction in size and no change to the substance itself, materials can display new qualities. • Polysaccharide-Modified MMT/ Modified MMT/ Polysaccharide – MNP, Lignin-Modified MMT Nanocomposites vs. Polyethyleneimineimine-Modified MMT have been compared for a Sustained Pesticide Delivery in this manuscript. • We anticipate that this description will aid researchers in selecting the best technique for developing pesticides and improving pesticide delivery.
Bioorthogonal Photo-Catalytic Activation of an Anti-Cancer Prodrug by Riboflavin
Authors: Yang Xin , Ma Limin , Shao Hongwei , Ling Xia , Yao Mengyu , Luo Guowen , Scoditti Stefano , Sicilia Emilia , Mazzone Gloria , Gao Meng , Tang Ben Zhong
Published: February 2022

Chemotherapies for cancer treatment usually suffer from poor targeting ability and serious side-effects. To improve the treatment efficiency and reduce side effects, photoactivatable chemotherapy has been recently proposed for precise cancer treatment with high spatiotemporal resolution. However, most photoactivatable prodrugs require decoration by stoichiometric photo-cleavable groups, which are only responsive to ultraviolet irradiation and suffer from low reaction efficiency. To tackle these challenges, we herein propose a bioorthogonal photo-catalytic activation strategy with riboflavin as the catalyst for in situ transformation of prodrug dihydrochelerythrine (DHCHE) prodrug into anti-cancer drug chelerythrine (CHE), which can efficiently kill cancer cells and inhibit in vivo tumor growth under light irradiation. Meanwhile, the photo-catalytic transformation from DHCHE into CHE was in situ monitored by green-to-red fluorescence conversion, which can be used for precise control of the therapeutic dose. The photocatalytic mechanism was also fully explored by means of density functional theory (DFT) calculations. We believe this imaging-guided bioorthogonal photo-catalytic activation strategy is promising for cancer chemotherapy in clinical applications.
Lifting the discrepancy between experimental results and the theoretical predictions for the catalytic activity of RuO2 (110) towards Oxygen Evolution Reaction
Authors: Divanis Spyridon , Frandsen Adrian , Kutlusoy Tugce , Rossmeisl Jan
Published: February 2022

Developing new efficient catalyst materials for the oxygen evolution reaction (OER) is essential for widespread proton exchange membrane water electrolyzer use. Both RuO2(110) and IrO2(110) have been shown to be highly active OER catalysts, however DFT predictions have been unable to explain the high activity of RuO2. We propose that this discrepancy is due to RuO2 utilizing a different reaction pathway, as compared to the conventional IrO2 pathway. This hypothesis is supported by comparisons between experimental data, DFT data and the proposed reaction model.
Olefin-surface interactions modulate the activity of silica-supported Mo-based olefin metathesis catalysts
Authors: Berkson Zachariah , Bernhardt Moritz , Schlapansky Simon , Benedikter Mathis , Buchmeiser Michael , Price Gregory , Sunley Glenn , Copéret Christophe
Published: February 2022

Molecularly defined and classical heterogenous Mo-based metathesis catalysts are shown to display distinct and unexpected reactivity patterns for the metathesis of long-chain α-olefins at low temperatures (< 100 °C). Namely, catalysts based on supported Mo oxo species, whether prepared via wet impregnation or surface organometallic chemistry (SOMC), exhibit strong activity dependencies on the α-olefin chain length, with slower reaction rates for longer substrate chain lengths. In contrast, molecular and supported Mo alkylidenes are highly active and do not display such dramatic dependence on chain length. 2D solid-state NMR analyses of post-metathesis catalysts, complemented by molecular dynamics calculations, evidence that the activity decrease observed for supported Mo oxo catalysts relates to the strong adsorption of internal olefin metathesis products due to interactions with surface Si-OH groups. Overall, this study shows that in addition to the nature and the number of active sites, the metathesis rates and overall catalytic performance depend on product desorption, even in the liquid phase with non-polar substrates. This study further highlights the need to consider adsorption when designing catalysts and the unique activity of molecularly defined supported metathesis catalysts prepared via SOMC.
Metathesis Cascade-Triggered Depolymerization of Enyne Self-Immolative Polymers
Authors: Yuan Jingsong , Giardino Gavin , Niu Jia
Published: February 2022

A novel class of enyne self-immolative polymers (SIPs) capable of me-tathesis cascade-triggered depolymerization is reported. Studies on mod-el compounds established 1,6-enyne structures for efficient metathesis cascade reactions. SIPs incorporating the optimized 1,6-enyne motif were prepared via both polycondensation and iterative exponential growth ap-proaches. These SIPs demonstrated excellent stability in strong acid, base, and nucleophiles, and can undergo efficient and complete depoly-merization once triggered by a metathesis catalyst. Further studies re-vealed that introducing a terminal alkene to the chain end of the enyne SIPs improved the depolymerization efficiency, and established their potential as stimuli-responsive materials.
Benchmarking molecular feature attribution methods with activity cliffs
Authors: Jiménez Luna José , Skalic Miha , Weskamp Nils
Published: February 2022

Feature attribution techniques are popular choices within the explainable artificial intelligence toolbox, as they can help elucidate which parts of the provided inputs used by an underlying supervised-learning method are considered relevant for a specific prediction. In the context of molecular design, these approaches typically involve the coloring of molecular graphs, whose presentation to medicinal chemists can be useful for making a decision of which compounds to synthesize or prioritize. The consistency of the highlighted moieties alongside expert background knowledge is expected to contribute to the understanding of machine-learning models in drug design. Quantitative evaluation of such coloring approaches, however, has so far been limited to substructure identification tasks. We here present an approach that is based on maximum common substructure algorithms applied to experimentally-determined activity cliffs. Using the proposed benchmark, we found that molecule coloring approaches in conjunction with classical machine-learning models tend to outperform more modern, deep-learning-based alternatives. However, none of the tested feature attribution methods sufficiently and consistently generalized when confronted with unseen examples.
Quantitative estimate of protein-protein interaction targeting drug-likeness
Authors: Kosugi Takatsugu , Ohue Masahito
Published: February 2022

The quantification of drug-likeness is very useful for screening drug candidates. The quantitative estimate of drug-likeness (QED) is the most commonly used quantitative drug efficacy assessment method proposed by Bickerton et al. However, QED is not considered suitable for screening compounds that target protein-protein interactions (PPI), which have garnered significant interest in recent years. Therefore, we developed a method called the quantitative estimate of protein-protein interaction targeting drug-likeness (QEPPI), specifically for early-stage screening of PPI-targeting compounds. QEPPI is an extension of the QED method for PPI-targeting drugs and developed using the QED concept, involving modeling physicochemical properties based on the information available on the drug. QEPPI models the physicochemical properties of compounds that have been reported in the literature to act on PPIs. Compounds in iPPI-DB, which comprises PPI inhibitors and stabilizers, and FDA-approved drugs were evaluated using QEPPI. The results showed that QEPPI is more suitable for the early screening of PPI-targeting compounds than QED. QEPPI was also considered an extended concept of "Rules of Four" (RO4), a PPI inhibitor index proposed by Morelli et al. To compare the discriminatory performance of QEPPI and RO4, we evaluated their discriminatory performance using the datasets of PPI-target compounds and FDA-approved drugs using F-score and other indices. Results of the F-score of RO4 and QEPPI were 0.446 and 0.499, respectively. QEPPI demonstrated better performance and enabled quantification of drug-likeness for early-stage PPI drug discovery. Hence, it could be used as an initial filter for efficient screening of PPI-targeting compounds, which has been difficult in the past.
Using collocation and solutions for a sum-of-product potential to compute vibrational energy levels for general potentials
Authors: Simmons Jesse , Carrington Tucker
Published: February 2022

It is easier to compute a vibrational spectrum when the potential energy surface (PES) is a sum-ofproducts (SOP). Many popular computational methods work only if the PES is a SOP. However, the most accurate PESs are not SOPs. We propose using collocation and solutions of the Schrödinger equation with a SOP PES to compute solutions on a corresponding general PES. This makes it possible to account for coupling and anharmonicity omitted from the SOP PES. We find that correcting energy levels computed on a SOP PES with collocation reduces differences with exact energy levels by about two orders of magnitude.
Development of a high-resolution mass spectrometry method for DNA adductomics investigation in colon cancer
Authors: La Barbera Giorgia , Dalmo Nommesen Katrine , Dragsted Lars Ove
Published: February 2022

Colorectal cancer (CRC) may develop after covalent modification of DNA by exogenous or endogenous genotoxic molecules coming from smoke, meat intake, inflammation or other factors. Several genotoxicants are known to cause DNA damage, but there is little evidence on their identity. DNA adductomics is a new research field, aiming to screen unknown DNA adducts by high resolution mass spectrometry (HRMS). However, due to the low abundance of DNA adducts, DNA adductomics presents several analytical challenges. In this work, a sensitive untargeted DNA adductomics method was developed by using ultra-high performance liquid chromatography (UHPLC) coupled via electrospray ionization source (ESI) to quadrupole-time of flight MS (Vion-qTOF). Mobile phases with ammonium bicarbonate gave the best signal enhancement. The MS capillary voltage, the cone voltage and the detector voltage mainly affected the response of the DNA adducts. A low adsorption vial was selected for reducing analyte loss. A hybrid surface coated HSST3 premier column showed a minimal adsorption of the DNA adducts. The optimized method was applied to analyse DNA from calf thymus and cat colon by performing a MSE acquisition screening for the loss of -dR, both in source and in the fragmentation spectra, and for the nucleobase fragment ions, to select the potential DNA adducts. Thirteen DNA adducts were observed in DNA from calf thymus and cat colon, showing good promise for the application of this untargeted method in future human studies.
Glenthenamines A–F: Enamine pyranonaphthoquinones from the Australian pasture plant-derived Streptomyces sp. CMB-PB042
Authors: Wu Taizong , Salim Angela , Cui Hui , Khalil Zeinab , Bernhardt Paul , Capon Robert
Published: February 2022

Chemical investigations into solid phase cultivations of an Australian sheep station pasture plant-derived Streptomyces sp. CMB-PB042, yielded the rare enamine naphthopyranoquinones BE-54238A (1) and BE-54238B (2), together with four new analogues, glenthenamines B–D (4–6) and F (8), and two handling artifacts, glenthenamines A (3) and E (7). Single crystal X-ray analyses of 1–2 resolved configurational ambiguities in the scientific literature, while detailed spectroscopic analysis and biosynthetic considerations assigned structures inclusive of absolute configuration to 3–8. We propose a plausible sequence of biosynthetic transformations linking structural and configurational features of 1–8, and apply a novel Schiff base "fishing" approach to detect a key deoxyaminosugar precursor. These enamine naphthopyranoquinone disclose a new P-gp inhibitory pharmacophore capable of reversing doxorubicin resistance in P-gp overexpressing colon carcinoma cells.
PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning
Authors: Xiao Sian , Tian Hao , Tao Peng
Published: February 2022

Allostery is a fundamental process in regulating proteins’ activity. The discovery, design and development of allosteric drugs demand for better identification of allosteric sites. Several computational methods have been developed previously to predict allosteric sites using static pocket features and protein dynamics. Here, we present a computational model using automated machine learning for allosteric site prediction. Our model, PASSer2.0, advanced the previous results and performed well across multiple indicators with 89.2% of allosteric pockets appeared among the top 3 positions. The trained machine learning model has been integrated with the Protein Allosteric Sites Server (https://passer.smu.edu) to facilitate allosteric drug discovery.
Polymorphism, Structure, and Nucleation of Cholesterol.H2O at Aqueous Interfaces and in Pathological Media: Revisited from a Computational Perspective
Authors: Shepelenko Margarita , Hirsch Anna , Varsano Neta , Addadi Lia , Kronik Leeor , Leiserowitz Leslie
Published: February 2022

We revisit the important issues of polymorphism, structure, and nucleation of cholesterol monohydrate, using first principles calculations based on dispersion-augmented density functional theory. For the lesser known monoclinic polymorph, we obtain a new, fully extended H-bonded network, comprising the sterol hydroxyl groups and water molecules in a structure akin to that of hexagonal ice. We show that the energy of the monoclinic and triclinic polymorphs is similar, strongly suggesting that kinetic and environmental effects play a significant role in determining polymorph nucleation. Furthermore, we find evidence in support of various O-H…O bonding motifs, in both polymorphs, that may result in structural disorder. We then rationalize what we believe is a single-crystal to single-crystal transformation of the monoclinic form on increased interlayer growth beyond that of a single cholesterol bilayer, interleaved by a water bilayer, and show that the ice-like structure is also relevant to the related cholestanol dihydrate (2H2O) crystal. Finally, we posit a possible role for cholesterol esters in the crystallization of cholesterol.H2O in pathological environments, with a composite of a bilayer of cholesteryl palmitate bound epitaxially as a nucleating agent to the monoclinic form of cholesterol.H2O.
Pharmaceutical Solid Form Formation via Vapour-Assisted Tumbling (VAT) – A Solvent Efficient Process with Potential Industrial Applications
Authors: Stirk Alexander Joseph , Souza Fabio E. S. , Gerster Jenny , Mir Fatemeh M. , Karadeolian Avedis , Rey Allan W.
Published: February 2022

Crystallisations on both the academic and industrial scale often use large volumes of solvent. In order decrease the environmental impact of such processes, new techniques must be discovered that increase the efficiency of the solvents used. Introduced here is a process that combines repurposed industry standard hardware and aspects of mechanochemistry to produce a technique we call “Vapour Assisted Tumbling” (VAT). Pharmaceutical and well-known cocrystals and salts were formed by tumbling the coformers in an atmosphere of vaporised solvent, in this study, methanol (MeOH). This was done inside a custom built analogue of an industrial rotary cone dryer (RCD). It was found that a desired solid form could be obtained as monitored by powder X-ray diffraction and differential scanning calorimetry. By repurposing industrial RCDs, it is feasible that solid forms can be crystallised with both minimal and reusable/recyclable solvent – drastically lowering the environmental impact of such transformations.
Formation of Pharmaceutical Salts and Cocrystals via Vapour-Assisted Tumbling (VAT) – A Solvent Efficient Process with Potential Industrial Applications
Authors: Stirk Alexander J. , Souza Fabio E. S. , Gerster Jenny , Mir Fatemeh M. , Karadeolian Avedis , Rey Allan W.
Published: February 2022

Crystallisations on both the academic and industrial scale often use large volumes of solvent. In order decrease the environmental impact of such processes, new techniques must be discovered that increase the efficiency of the solvents used. Introduced here is a process that combines repurposed industry standard hardware and aspects of mechanochemistry to produce a technique we call “Vapour Assisted Tumbling” (VAT). Pharmaceutical and well-known cocrystals and salts were formed by tumbling the coformers in an atmosphere of vaporised solvent, in this study, methanol (MeOH). This was done inside a custom built analogue of an industrial rotary cone dryer (RCD). It was found that a desired solid form could be obtained as monitored by powder X-ray diffraction and differential scanning calorimetry. By repurposing industrial RCDs, it is feasible that solid forms can be crystallised with both minimal and reusable/recyclable solvent – drastically lowering the environmental impact of such transformations.
A directed sampling approach for modelling the structural and electronic properties of amorphous alumina
Authors: Harper Angela F , Emge Steffen P , Magusin Pieter C M M , Grey Clare P , Morris Andrew J
Published: February 2022

Advancing the next generation of materials for solid-state devices requires an understanding of their underlying electronic structure; yet the amorphous nature of many materials hinders progress in creating an atomic-level model. One such material is amorphous alumina, which is used to enhance performance in electronic devices from Li-ion batteries to perovskite solar cells. We develop a method which captures local properties of alumina through experimentally informed direct sampling of static configurations from ab initio molecular dynamics. This model is validated with solid-state nuclear magnetic resonance and X-ray absorption spectroscopy, calculated from the first principles level of theory. We finally construct an average electronic density of states for alumina from our model and observe two highly localized states at the conduction band edge.
Surfactant-free syntheses and pair distribution function analysis of osmium nanoparticles
Authors: Juelsholt Mikkel , Quinson Jonathan , Kjær Emil , Wang Baiyu , Pittkowski Rebecca , Cooper Susan , Kinnibrugh Tiffany , Simonsen Søren , Theil Kuhn Luise , Escudero-Escribano Maria , Jensen Kirsten
Published: February 2022

A surfactant-free synthesis of precious metal nanoparticles performed in low boiling point solvents and in alkaline conditions has been reported recently. This strategy presents several advantages over alternative colloidal syntheses. The resulting nanoparticles are readily relevant for applications like catalysis and the synthetic process is compatible with large scale production. Alkaline mono-alcohols are here investigated as solvent and reducing agents to obtain colloidal Os nanoparticles by this low temperature (< 100 °C) surfactant-free synthesis. The effect of precursor (OsCl3 or H2OsCl6), precursor concentration (up to 100 mM), solvent (methanol or ethanol), presence or absence of base (NaOH) and addition of water (0 to 100 v.%) on the resulting nanomaterials is discussed. It is fond that no base is required to obtain Os nanoparticles as opposed to the case of Pt NPs for instance. The robustness of the synthesis for concentration of precursor up to 100 mM allows to perform X-ray total scattering with pair distribution function (PDF) analysis that shows that the 1-2 nm hcp NPs forms from chain-like [OsOxCly]-complexes.
A Luminescent 1D Silver Polymer Containing [2.2]Paracyclophane Ligands
Authors: Mackenzie Campbell , Delforce Lucie , Rota Martir Diego , Cordes David , Slawin Alexandra , Zysman-Colman Eli
Published: February 2022

[2.2]Paracyclophane scaffolds have seen limited use as building blocks in supramolecular chemistry. Here, we report the synthesis and characterization of a 1D coordination polymer consisting of silver(I) ions bound to a [2.2]paracyclophane scaffold functionalized with two 4-pyridyl units. The structure of the polymer has been determined from single crystal X-ray diffraction analysis and reveals two different silver coordination motifs that alternate along the 1D coordination polymer. The coordination polymer exhibits strong blue and sky-blue fluorescence in solution and in the crystalline solid state, respectively.
A Crystalline Tri-thorium Cluster: When Metal σ-Aromaticity Just Isn’t Enough
Authors: Szczepanik Dariusz
Published: February 2022

Very recently, Liddle and coworkers extended the range of aromaticity to a record seventh row of the periodic table by successful isolation of the crystalline actinide cluster 3 containing at its heart the σ-aromatic tri-thorium ring. In this study we prove that the authors have misinterpreted the experimental Raman spectrum of 3, which eventually led to the wrong conclusions about the role of the σ-aromatic tri-thorium bonding in the synthesized cluster. We demonstrate that the thorium-thorium bond in 3 is not very different from the already known extremely weak actinide-actinide bonds, and the marginal σ-aromatic stabilization in the Th3 ring makes it hardly distinguishable from ordinary non-aromatic rings. Also, we show that the multicenter charge-shift bonding in the Th3Cl6 cage is a vital factor that determines the uniqueness and remarkable thermodynamic stability of 3. By clarifying the misleading conclusions of the original Nature paper and drawing special attention to the essential stabilizing role of actinide-halogen charge-shift bonding, this study may have broader implications for understanding the chemistry of actinides and future attempts to design and synthesize new stable actinide complexes.
A σ-Aromatic Tri-Thorium Bonding: Does It Really Exist?
Authors: Szczepanik Dariusz
Published: February 2022

The experimental realization of actinide-actinide bonding in isolable molecules has been one of the main targets of synthetic actinide chemistry for decades. Very recently, Boronski et al. reported the first thorium-thorium bonding in a crystalline cluster (3) prepared and isolated under normal experimental conditions. The electron spin resonance and the superconducting quantum-interference device magnetometry revealed a diamagnetic ground-state with two electrons equally distributed over the tri-thorium ring at the heart of 3, and the recorded Raman spectrum allegedly confirmed the existence of a three-center two-electron (3c-2e) bond. However, the observed broad inelastic scattering bands between 60 and 135 cm-1, originally assigned by the authors to thorium-thorium vibrations, represent in fact the combination of thorium-chlorine stretching modes, and they establish the existence of a unique charge-shift actinide-halogen bonding rather than the σ-aromatic (delocalized) actinide-actinide bonding as claimed in the original article.
PdO self-assembly on zeolite SSZ-13 with rows of O3Al(IV)OH selectively incorporated in PdO(101) facets for moisture-resistant methane oxidation
Authors: Kovarik Libor , Jaegers Nicholas , Szanyi Janos , Derewinski Miroslaw , Wang Yong , Khivantsev Konstantin
Published: February 2022

We describe an efficient way to prepare moisture-tolerant methane (hydrocarbon) combustion catalysts based on PdO nanoparticles supported on siliceous SSZ-13 zeolite. Only zeolites with high Si/Al ratios >15 are hydrophobic enough to exclude the Pd from the micropores while forming well-faceted PdO nanoparticles. Simultaneously, during self-assembly mobile Al hydroxo species get incorporated into the as-formed PdO nanoparticles. For the first time, we reveal selective incorporation of rows of O3Al(IV)-OHbridging aluminum hydroxo-species into the (101) facets of PdO nanoparticles that form during thermal self-assembly in Pd/SSZ-13 using state-of-the-art atomically-resolved HAADF-STEM imaging, solid-state NMR, DFT calculations and reactivity measurements. The Al+3-OH moieties form atom-thin rows in place of tri-coordinate Pd ions Pd+2 in Pd1O3 on (101) facets: these tri-coordinate Pd1+2O3 are responsible for C-H bond dissociation of methane and hydrocarbons during catalytic methane oxidation. However, on unmodified or non-zeolite supported PdO nanoparticles in the presence of water vapor from engine exhaust, water competes with methane by forming a deactivated Pdtetra(OH)(H2O)Pdtetra site with two water molecules on contiguous 3-coordinate Pd, which is not active for C-H bond activation. When Al-OH moieties are present in place of some tri-coordinate Pd1O3 sites, water dissociation becomes kinetically unfavorable due to disruption of Pdtetra(OH)(H2O)Pdtetra species formation. Consequently, our catalytic measurements reveal a significantly more stable performance of such catalysts in methane combustion in the presence of water vapor. Our findings provide an unprecedented atomic-level insight into structure-property relationships for supported PdO materials in catalytic methane oxidation and offer a new strategy to prepare moisture-tolerant Pd-containing methane combustion catalysts for green-house gas mitigation by selectively doping atomically thin rows of non-precious metal into specific facets of PdO.
Study of Ruthenium-Contamination Effect on Oxygen Reduction Activity of Platinum-based PEMFC and DMFC Cathode Catalyst
Authors: Kaplan Dima , Tereshchuk Polina , Olewsky Chen , Keinan Liz , Ben Yehuda Ohad , Shviro Meital , Natan Amir , Peled Emanuel
Published: February 2022

We outline a systematic experimental and theoretical study on the influence of ruthenium contamination on the oxygen reduction activity (ORR) of a Pt/C catalyst at potentials relevant to a polymer electrolyte fuel cell cathode. A commercial Pt/C catalyst was contaminated by different amounts of ruthenium, equivalent to 0.15-4 monolayers. The resulting ruthenium-contaminated Pt/C powders were characterized by Energy–Dispersive X–ray Spectroscopy (EDS), X–ray Photoelectron Spectroscopy (XPS) and Scanning Transmission Electron Microscopy (STEM) to verify ruthenium contamination. A rotating disk electrode (RDE) technique was used to study the influence of ruthenium on oxygen reduction kinetics. Density functional theory (DFT) calculations were performed to estimate the oxygen reduction activity of the platinum surface with increasing ruthenium coverage, simulating ruthenium-contaminated Pt/C. The binding energies of O and OH on the surfaces were used for activity estimations. It was found that the specific activity of the ORR at 0.85V vs RHE exhibited a pseudo-exponential decay with increased ruthenium contamination, decreasing by ~45% already at 0.15 monolayer-equivalent contamination. The results of the DFT calculations were qualitatively in line with experimental findings, verifying the effect of O and OH binding energies and the oxophilic nature of ruthenium on ORR and the ability of the chosen approach to predict the effect of ruthenium contamination on ORR on platinum.
A Theoretical Analysis of Coherent Cross-Peaks in Polarization Selective 2DIR for Detection of Cross-α Fibrils
Authors: Edun Dean , Cracchiolo Olivia , Serrano Arnaldo
Published: February 2022

The coupled amide-I vibrational modes in peptide systems such as fibrillar aggregates can often provide a wealth of structural information, though the associated spectra can be difficult to interpret. Using exciton scattering calculations, we characterized the polarization selective 2DIR peak patterns for cross-α peptide fibrils, a challenging system given the similarity between the monomeric and fibrillar structures, and interpret the results in light of recently collected 2D data on the cross-α peptide PSMα3. We find that stacking of α-helices into fibrils couples the bright modes across helical subunits, generating three new Bloch-like extended excitonic states that we designate A⏊, E∥, and E⏊. Coherent superpositions of these states in broad-band 2DIR simulations lead to characteristic signals that are sensitive to fibril length, and match the experimental 2DIR spectra.
Fast Sonochemical Exfoliation of Hematene type Sheets and Flakes from Hematite Nanoarchitectures Shows Enhanced Photocurrent Density
Authors: Agarwal Purvika , BORA Debajeet K.
Published: February 2022

Here, we describe the exfoliation of 2D Hematene single layer from a Hematite nanoparticle-based nanoarchitectures obtained by a water-mediated synthesis route with the ultrasonication method in a brief period which is 5 min. The Hematene obtained shows the fine structure of honeycomb lattice resembling the Hematite hexagonal crystallographic pattern. Here, we found that the ultrasonicated Hematite film with Hematene flakes shows enhanced current density than the pristine Hematite film which can be extended further to increase the efficiency of well-performing or champion photoanode for the artificial photosynthesis application. Besides this, a new photocurrent transient spike is obtained, which we ascribed as the generation of the sub-surface state by Hematene flakes. Followed by this, we have also deciphered a qualitative predictive mechanism for the fast exfoliation of Hematene in which surface energies and hydroxylation of crystal facets are proposed to be the factor responsible for the quick exfoliation process.
A Convenient Synthesis and Spectral Studies of Diamines Derivatives
Authors: Gondi Sudershan Reddy , Jacobsson Michael B. , Rissing Christiana Julia , SON DAVID Y
Published: February 2022

A new series of substituted anthranilic esters derivatives linked with a 1,3-dithiolane andbenzyloximino moiety was synthesized using the simple esterfication reaction and products werefully characterized. The isolated yields of these compounds range from 59 to 96%. 1,3-dithiolane ester and the benzyloxy substituted diamine derivatives are white solids and stable toair and moisture. The synthesized compounds can be exhibits UV-vis absorption properties bytheir structures with a amine or amide group, It is observed that absorption maximum is excellentfor 2,6-disubstituted benzyloxy esters which can be explained by electron transfer or conjugationis steric effect in ortho substitution from the amino group and the amide group.
Constant inner potential DFT for modelling electrochemical systems under constant potential and bias
Authors: Melander Marko , Wu Tongwei , Honkala Karoliina
Published: February 2022

Electrochemical interfaces and reactions play a decisive role in e.g. clean energy conversion but understanding their complex chemistry remains an outstanding challenge. Constant potential or grand canonical ensemble (GCE) simulations are indispensable for unraveling the properties of electrochemical processes as a function of the electrode potential. Currently, constant electrode potential calculations at the density functional theory (DFT) level are carried out by fixing the Fermi level of the simulation cell. However, the Fermi level from DFT calculations does does not always reflect the experimentally controlled electrode potential or describe the thermodynamic independent variable in GCE-DFT i.e the electrochemical potential of an electron reservoir. Here we develop and implement the constant inner potential (CIP) method as a more robust and general approach to GCE-DFT simulations of electrochemical systems under constant potential or bias conditions. The CIP is shown to directly control the reservoir electron electrochemical potential making the method widely applicable in simulating electrochemical interfaces. We demonstrate that the CIP and Fermi level GCE-DFT approaches are equivalent for metallic electrodes and inner sphere reactions. The CIP method is shown to be applicable in simulating also semiconductor electrodes, outer sphere reactions, and a biased two-electrode cell for which the Fermi level approach does not reflect the experimental electrode potential. Unlike the Fermi level method, CIP does not require any electronic structure information as only the inner potential is needed, which makes the approach more compatible with classical force field or machine learning potentials. The CIP approach emerges as a general GCE DFT method to simulate (photo)electrochemical interfaces from first principles.