bluuebunny/crossref_metadata_2025 huggingface dataset:
Combination of pose and rank consensus in docking-based virtual screening: the best of both worlds
Authors: Scardino Valeria , Bollini Mariela , Cavasotto Claudio
Published: February 2022

The use of high-throughput docking (HTD) in the drug discovery pipeline is today widely established. In spite of methodological improvements in docking accuracy (pose prediction), scoring power, ranking power, and screening power in HTD remain challenging. In fact, pose prediction is of critical importance in view of the pose-dependent scoring process, since incorrect poses will necessarily decrease the ranking power of scoring functions. The combination of results from different docking programs (consensus scoring) has been shown to improve the performance of HTD. Moreover, it has been also shown that a pose consensus approach might also result in database enrichment. We present a new methodology named Pose/Ranking Consensus (PRC) that combines both pose and ranking consensus approaches, to overcome the limitations of each stand-alone strategy. This approach has been developed using four docking programs (ICM, rDock, Auto Dock 4, and PLANTS; the first one is commercial, the other three free). We undertook a thorough analysis for the best way of combining pose and rank strategies, and applied the PRC to a wide range of targets sampling different protein families with a variety of binding site properties. Our approach exhibits an improved systematic performance in terms of enrichment factor and hit rate with respect to either pose consensus or consensus ranking alone strategies at a lower computational cost, while always ensuring the recovery of a suitable number of ligands. An analysis using four free docking programs (replacing ICM by Auto Dock Vina) displayed comparable results.
Combinatorial Polycation Synthesis and Causal Machine Learning Reveal Divergent Polymer Design Rules for Effective pDNA and Ribonucleoprotein Delivery
Authors: Kumar Ramya , Le Ngoc , Oviedo Felipe , Brown Mary E. , Reineke Theresa M.
Published: February 2022

The development of polymers that can replace engineered viral vectors in clinical gene therapy has proven elusive despite the vast portfolios of multifunctional polymers generated by advances in polymer synthesis. Functional delivery of payloads such as plasmids (pDNA) and ribonucleoproteins (RNP) to various cellular populations and tissue types requires design precision. Here, we systematically screen a combinatorially designed library of 43 well-defined polymers, ultimately identifying a lead polycationic vehicle (P38) for efficient pDNA delivery. Further, we demonstrate the versatility of P38 in co-delivering spCas9 RNP and pDNA payloads to mediate homology directed repair as well as in facilitating efficient pDNA delivery in ARPE-19 cells. P38 achieves nuclear import of pDNA and eludes lysosomal processing far more effectively than a structural analog that does not deliver pDNA as efficiently. To reveal the physicochemical drivers of P38's gene delivery performance, SHapley Additive exPlanations (SHAP) are computed for nine polyplex features, and a causal model is applied to evaluate the average treatment effect of the most important features selected by SHAP. Our machine learning interpretability and causal inference approach derives structure-function relationships underlying delivery efficiency, polyplex uptake, and cellular viability, and probes the overlap in polymer design criteria between RNP and pDNA payloads. Together, combinatorial polymer synthesis, parallelized biological screening, and machine learning establish that pDNA delivery demands careful tuning of polycation protonation equilibria while RNP payloads are delivered most efficaciously by polymers that deprotonate cooperatively via hydrophobic interactions. These payload-specific design guidelines will inform further design of bespoke polymers for specific therapeutic contexts.
Temperature Cycling Enables Efficient 13C SABRE-SHEATH Hyperpolarization and Imaging of [1-13C]Pyruvate
Authors: TomHon Patrick , Abdulmojeed Mustapha , Adelabu Isaiah , Nantogma Shiraz , Kabir Mohammad Shah Hafez , Lehmkuhl Sören , Chekmenev Eduard Y. , Theis Thomas
Published: February 2022

Current metabolic imaging in humans is dominated by positron emission tomography (PET) methods. An emerging non-ionizing alternative for molecular imaging is hyperpolarized MRI. In particular, imaging of hyperpolarized 13C-pyruvate is a leading candidate because pyruvate is innocuous and has a central role in metabolism. However, simi-lar to PET, hyperpolarized MRI with dynamic nuclear polarization (DNP) is complex, costly and requires complex in-frastructure. In contrast, signal amplification by reversible exchange (SABRE) is a fast, cheap, and scalable hyperpo-larization technique. In particular, SABRE in SHield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH) transfers polarization from parahydrogen to 13C in pyruvate, however, to date, SABRE-SHEATH of 13C-pyruvate was limited in polarization levels relative to DNP (1.7% with SABRE-SHEATH vs. ~60% with DNP). Here we introduce a temperature cycling method for SABRE-SHEATH that enables >10% polarization on [1-13C]pyruvate, sufficient for successful in vivo experiments. First, at lower temperatures, ~20% polarization is accumulated on SABRE-catalyst bound pyruvate, which is subsequently released into free pyruvate in solution at elevated temperatures. We take ad-vantage of the achieved polarization to demonstrate first 13C pyruvate images with a cryogen-free MRI system operat-ed at 1 T. This illustrates that inexpensive hyperpolarization methods can be combined with low-cost MRI systems to obtain a broadly available, yet highly sensitive metabolic imaging platform.
A simple setup miniaturization with multiple benefits for Green Chemistry in nanoparticle synthesis
Authors: Mathiesen Jette , Cooper Susan , Anker Andy , Kinnibrugh Tiffany , Jensen Kirsten , Quinson Jonathan
Published: February 2022

The development of nanomaterials often relies on wet-chemical syntheses performed in reflux-setups using round-bottom-flasks. An alternative approach to synthesize nanomaterials is here presented that uses glass tubes designed for NMR analysis as reactors. This approach uses less solvent, uses less energy, generates less waste, provides safer conditions, is less prone to contamination and is compatible with high throughput screening.
A simple setup miniaturization with multiple benefits for Green Chemistry in nanoparticle synthesis
Authors: Mathiesen Jette , Cooper Susan , Anker Andy , Kinnibrugh Tiffany , Jensen Kirsten , Quinson Jonathan
Published: February 2022

The development of nanomaterials often relies on wet-chemical syntheses performed in reflux-setups using round-bottom-flasks. An alternative approach to synthesize nanomaterials is here presented that uses glass tubes designed for NMR analysis as reactors. This approach uses less solvent, uses less energy, generates less waste, provides safer conditions, is less prone to contamination and is compatible with high throughput screening. The benefits of this approach are illustrated by an in breadth study with the synthesis of gold, iridium, osmium and copper sulfide nanoparticles.
Deciphering the mechanism of the Ni-photocatalyzed C‒O cross-coupling reaction using a tridentate pyridinophane ligand
Authors: Mirica Liviu , Na Hanah
Published: February 2022

Photoredox nickel catalysis has emerged as a powerful strategy for cross-coupling reactions. Although the involvement of paramagnetic Ni(I)/Ni(III) species as active intermediates in the catalytic cycle has been proposed, a thorough spectroscopic investigation of these species is lacking. Herein, we report a new class of tridentate pyridinophane ligands RN3 that allow for detailed mechanistic studies of the photocatalytic C–O coupling reaction. The derived (RN3)Ni complexes are active catalysts under mild conditions and without an additional photocatalyst. We also provide direct evidence for the key steps involving paramagnetic Ni species in the proposed catalytic cycle: the oxidative addition of an aryl halide to a Ni(I) species, the ligand exchange/transmetalation at a Ni(III) center, and the C–O reductive elimination from a Ni(III) species. Overall, the present work suggests the RN3 ligands are a practical platform for mechanistic studies of Ni-catalyzed reactions and for the development of new catalytic applications.
Pb-oxo Interactions in Uranyl Hybrid Materials: a Combined Experimental and Computational Analysis of Bonding and Spectroscopic Properties
Authors: Brager Dominique M. , Nicholas Aaron D. , Schofield Mark H. , Cahill Christopher L.
Published: February 2022

Reported are the syntheses and characterization of six new heterometallic UO22+/Pb2+ compounds. These materials feature rare instances of M-oxo interactions, which influence bonding properties of the uranyl cation. The spectroscopic effects of these interactions were measured using diffuse reflectance, luminescence and Raman spectroscopy. Computational density functional theory (DFT) based natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) methods indicate interactions arise predominantly through charge transfer between cationic units via the electron donating uranyl O spx lone pair orbitals and electron accepting Pb2+ p orbitals. The interaction strength varies as a function of Pb-oxo interaction distance and angle with energy values ranging from ranging from 0.47 kcal/mol in the longer contacts to 21.94 kcal/mol in the shorter contacts. Uranyl units with stronger interactions display an asymmetric bond weakening and a loss of covalent character in the U=O bonds interacting closely with the Pb2+ ion. Luminescence quenching is observed in cases where strong Pb-oxo interactions are present, and is accompanied by significant red-shifting of the uranyl symmetric Raman stretch. Changes to inner sphere uranyl bonding manifest as a weakening of the U=O bond as a result of interaction with the Pb2+ ion.
Comparison of 2D versus 3D diffusion analysis at Nanowire Electrodes: Finite element analysis and experimental study
Authors: O'Sullivan Benjamin , O'Sullivan Shan , Naruyan Tarun , Shao Han , Patella Bernardo , Seymour Ian , Inguanta Rosalinda , O'Riordan Alan
Published: February 2022

In electroanalysis, finite element simulations of electrochemical processes occurring at electrodes are used to provide key insight into experimental design in relation to diffusion profiles and expected currents. The diffusion domain approach (DDA) offers a means of reducing a three dimensional design to two dimensions to ease computational demands. However, the DDA approach can be limited when basic assumptions, for example that all electrodes in an array are equivalent, are incorrect. Consequently, to get a more realistic view of molecular diffusion to nanoelectrodes, it is necessary to undertake simulations in 3D. In this work, two and three dimensional models of electrodes comprising of (i) single nanowires, (ii) arrays of nanowires and (iii) interdigitated arrays of nanowires operating in generator-collector mode, are undertaken and compared to experimental results obtained from fabricated devices. The 3D simulations predict a higher extracted current for a single nanowires and diffusionally independent nanowire arrays when compared to 2D simulations since, unlike the 2D model, they take into account molecular diffusion to and from the nanowire termini. This current difference was observed to increase with increasing electrode width and decrease with electrode length. When the nanowire arrays were diffusionally overlapped, they behaved as an electrode of larger width, and the divergence between the two models increased. By contrast, in generator-collector mode, using interdigitated nanowire arrays, the difference between extracted current values obtained using two models was significantly lower. Simulations indicated however that a higher collection efficiency was predicted by the 2D model when compared to the 3D model. Electrochemical experiments were undertaken to confirm the simulation study and demonstrated that the extracted currents from 3D simulations more closely mapped onto experimentally measured currents.
Asymmetric synthesis of heterocyclic chloroamines and aziridines by enantioselective protonation of catalytically generated enamines
Authors: McLean Liam , Ashford Matthew , Fyfe James , Slawin Alexandra , Leach Andrew , Watson Allan
Published: February 2022

We report a method for the synthesis of chiral vicinal chlo-roamines via asymmetric protonation of catalytically gener-ated prochiral chloroenamines using chiral Brønsted acids. The process is highly enantioselective, with the origin of asymmetry and catalyst substituent effects elucidated by DFT calculations. We show the utility of the method as an approach to the synthesis of a broad range of heterocycle-substituted aziridines by treatment of the chloroamines with base in a one-pot process, as well as the utility of the process to allow access to vicinal diamines.
A Tri-Layered Hydrogel Scaffold for Vocal Fold Tissue Engineering
Authors: Tindell R. Kevin , McPhail Michael J. , Myers Cheryl , Neubauer Juergen , Hintze Justin M. , Lott David G. , Holloway Julianne L.
Published: February 2022

The lamina propria within the vocal fold (VF) is a complex multi-layered tissue that increases in stiffness from the superficial to deep layer, where this characteristic is crucial for VF sound production. Tissue engineered scaffolds designed for VF repair must mimic the biophysical nature of the native vocal fold and promote cell viability, cell spreading, and vibration with air flow. In this study, we present a unique tri-layered, partially-degradable hydrogel scaffold that mimics the multi-layered structure of the VF lamina propria. Using thiol-norbornene photochemistry, tri-layered hydrogel scaffolds were fabricated via layer-by-layer stacking with increasing polymer concentration from the top to middle to deep layer. Mechanical analysis confirmed hydrogel modulus increased with increasing polymer concentration. Partially-degradable hydrogels promoted high cell viability and cell spreading in 3D as assessed via live/dead and cytoskeleton staining, respectively. Importantly, partially-degradable hydrogels maintained some degree of the 3D polymer network following protease exposure, while still enabling encapsulated cells to remodel their local environment via protease secretion. Finally, the tri-layered hydrogel scaffold successfully vibrated and produced sound in proof-of-concept air flow studies. This work represents a critical first step towards the design of a multi-layered, hydrogel scaffold for vocal fold tissue engineering.
Cascaded energy landscape as a key driver for slow yet efficient charge separation with small energy offset in organic solar cells
Authors: Natsuda Shin-ichiro , Saito Toshiharu , Shirouchi Rei , Sakamoto Yuji , Takeyama Taiki , Tamai Yasunari , Ohkita Hideo
Published: February 2022

Recent studies have shown that efficient free carrier (FC) generation with a small voltage loss can be achieved in organic solar cells (OSCs); however, the photophysical insights underpinning this remain unclear. Herein, we examined the mechanisms underlying the FC generation in a state-of-the-art OSC consisting of PM6 and Y6 as an electron donor and electron acceptor, respectively, wherein the energy offset between the lowest excited singlet state and the charge transfer state is as small as ~0.1 eV. We used transient absorption spectroscopy to track the time evolution of electroabsorption caused by electron–hole pairs generated at donor/acceptor interfaces. Upon photoexcitation of the lower-bandgap Y6, we observed slow yet efficient spatial charge dissociation on a time scale of picoseconds. Based on temperature dependence measurements, we found that this slow yet efficient FC generation is driven by downhill energy relaxation of charges through the energy cascade generated near the interfaces.
Multivariate sodalite Zeolitic Imidazolate frameworks: a direct solvent-free synthesis
Authors: López-Cabrelles Javier , Miguel-Casañ Eugenia , Esteve-Rochina Maria , Andres-Garcia Eduardo , Vitórica-Yrezábal Iñigo , Calbo Joaquin , Minguez Espallargas Guillermo
Published: February 2022

Different mixed-ligand Zeolitic Imidazolate Frameworks (ZIFs) with sodalite topology, i.e. isoreticular to ZIF-8, unachievable by conventional synthetic routes, have been prepared using a solvent-free methodology. In particular, the versatility of this method is demonstrated with three different metal centres (Zn, Co and Fe) and binary combinations of three different ligands (2-methylimidazole, 2-ethylimidazole and 2-methylbenzimidazole). One combination of ligands, 2-ethylimidazole and 2-methylbenzimidazole, results in the formation of SOD frameworks for the three metal centres despite this topology not being obtained for the individual ligands. Theoretical calculations confirm that this topology is the lowest in energy upon ligand mixing.
Non-halogenated Imidazolium and Phosphonium-based Surface-Active Ionic Liquids as Electrolytes for Supercapacitors
Authors: Jain Preeti
Published: February 2022

We report a comparative analysis of three novel non-halogenated surface-active ionic liquids (SAILs), which consist of a surface-active anion, 2-ethylhexyl sulfate ([EHS]-), and phosphonium or imidazolium cations: tetrabutylphosphonium ([P4,4,4,4]+), trihexyl(tetradecyl)phosphonium ([P6,6,6,14]+), and 1-methyl-3-hexylimidazolium ([C6C1Im]+). We explored thermal properties (degradation, melting and crystallisation temperatures) of these novel SAILs and their electrochemical properties (ionic conductivity and electrochemical potential window, ECW). These SAILs were tested as electrolytes in a multi-walled carbon nanotubes (MWCNTs)-based supercapacitor at various temperatures from 253 to 373 K and their electrochemical performance as a function of temperature was compared. We found that the supercapacitor cell with [C6C1Im][EHS] as an electrolyte has shown a higher specific capacitance (Celec in F g-1), a higher energy density (E in W h kg-1), and a higher power density (P in kW kg-1) as compared to the other studied SAILs, [P4,4,4,4][EHS], [P6,6,6,14][EHS] and [N8,8,8,8][EHS] (from previous our study) at a temperature range from 253 to 373 K. The supercapacitor with an MWCNT-based electrode and [C6C1Im][EHS], [P4,4,4,4][EHS] and [P6,6,6,14][EHS] as electrolytes showed a specific capacitance of 148, 90 and 47 F g-1 (at the scan rate of 2 mV s-1) with an energy density of 82, 50 and 26 W h kg-1 (at 2 mV s-1), respectively, all at 298 K. For latter three SAILs, the temperature effect can be seen by a two to three-fold increase in the specific capacitance of the cell and the energy density values: 290, 198 and 114 F g-1 (at 2 mV s-1) and 161, 110 and 63 Wh kg-1 (at 2 mV s-1), respectively, at 373 K. The solution resistance (Rs), charge transfer resistance (Rct), and equivalent series resistance (ESR) also decreased with an increase in temperature for all SAILs in this study. These new SAILs can potentially be used for high-temperature electrochemical applications, such as supercapacitors for high energy storage due to a reasonably high specific capacitance and enhanced energy and power density, and wider ECWs as compared to molecular organic and aqueous electrolytes. Specifically, [C6C1Im][EHS] and [P4,4,4,4][EHS], are the best candidates among other “EHS”-based SAILs in this and our previous study, as electrolytes in supercapacitors.
Fidelity of Robotic Chemical Operations of Homogenous and Heterogeneous Reactions
Authors: Wang Guoqiang , Xin Bo , Wang Gaobo , Zhang Yong , Lu Yunwen , Guo Lin , Li Shuhua , Chen Chunlin , Cheng Xu , Ma Jing
Published: February 2022

Chemical synthesis always involves laborious and time-consuming operations. Autonomous chemical synthesis systems can liberate experimentalists from those routine tasks, but the design of automatic chemical reaction machines is of great challenge. We describe herein the development of a real-life automatic chemical operation platform by using a coordinated multi-robot system with artificial intelligence and machine learning methods. The capacities of this platform were demonstrated by its application in condensation reaction of 2,4-dinitrophenyldrazine with formaldehyde, and automatic catalyst evaluation of a heterogeneous aza Diels-Alder reaction, suggesting the designed machine is applicable to both homogenous and heterogeneous chemical reactions. Besides, the excellent repeatability and reproducibility of robotic tests on these two model reactions indicate the great promise of massive transfer of manual to automatic operation.
Synthesis of Azalurenone Alkaloids by Pd- mediated Intramolecular Oxidative Cyclisation Protocol
Authors: Ray Jayanta Kumar
Published: February 2022

In this paper we present the synthesis of different substituted azafluorenone via oxidative intra-molecular Heck cyclization protocol. The Heck precursor alcohols were synthesised via reaction of the Grignard reagents of corresponding iodides upon 2-bromopyridine-3-carboxaldehyde The Grignard reagents were easily prepared from fresh magnesium turnings activated by pinch of iodine and their corresponding halides (iodide or bromide) in refluxing dry ether medium. Then these freshly prepared Grignard reagents were added drop wise into an ice-cold ethereal solution of 2-bromoprydine-3-carboxaldehyde , which gave our desired Heck precursor alcohols in quantitative yields
A Computational Study on the Ca2+ Solvation, Coordination Environment, and Mobility in Electrolytes for Calcium Ion Batteries
Authors: Biria Saeid , Pathreeker Shreyas , Hosein Ian D.
Published: February 2022

Calcium (ion) batteries are promising next-generation energy storage systems, owing to their numerous benefits in terms of performance metrics, low-cost, mineral abundance, and economic sustainability. A central and critical area to the advancement of the technology is the development of suitable eletrolytes that allow for good salt solubility, ion mobility, electrochemical stability, and reversible redox activity. At this time, the study of different solvent-salt combinations is very limited. Here, we present a computational study on the coordination environment, solvation energetics, and diffusivity of calcium ions over a range of pertinent ionic liquids, cyclic and acylic alkyl carbonates, and specific alkyl nitriles and alkyl formamides, using the salts calcium bis(trifluoromethylsulfonyl)imide (Ca(TFSI)2) and calcium perchlorate (Ca(ClO4)2). Key findings are that several solvents from different solvent classes present comparable solvation environments and mobilities. Ca(TFSI)2 is prefered over Ca(ClO4)2 owing to the former’s mix coordination of Ca2+ to O and N atoms. Ionic liquids with alkyl sulfonate anions provide better coordation over TFSI, which leads to greater diffusivity. Binary organic mixtures (carbonates) provide the best solvation of Ca2+, however, single organic solvents also provide good solvation, such as EC, THF and DMF, as well as some acyclic carbonates. Ion pairing with the salt anion is always present, but can be mitigated through solvent selection, which also correlates to greater mobility; however, there are examples in which strong ion pairing is not significantly adverse to diffusivity. The solvent incorporate into the solvation structure with binary organic mixtures correlates well with the solvation capabilities of the individual solvents. Finally, we show that ionic liquids (specifically alkyl imidazole (cation) alkyl sulfonate (anion) ionic liquids) do not decompose when coordinating at a Ca metal interface, which indicates its promising stability. Overall, this study contributes further generalized understanding of the correlation between solvent and salt and the resultant Ca2+ complexes and Ca2+ mobility in a range of electrolytes, and reveals a range of possible solvents suitable for exploration in calcium (ion) batteries.
Quantifying Order during Field-driven Alignment of Colloidal Semiconductor Nanorods
Authors: Ratnaweera Rivi , Rodríguez Ortiz Freddy , Gripp Nicholas , Sheldon Matthew
Published: February 2022

Aligning large populations of colloidal nanorods (NRs) into ordered assemblies provides a strategy for engineering macroscopic functional materials with strong optical anisotropy. The bulk optical properties of such systems depend not only on the individual NR building blocks, but also on their meso- and macroscale ordering, in addition to more complex inter-particle coupling effects. Here, we investigate the dynamic alignment of colloidal CdSe/CdS NRs in the presence of AC electric fields by measuring concurrent changes in optical transmission. Our work identifies two distinct scales of interaction that give rise to the field-driven optical response: (1) the spontaneous mesoscale self-assembly of colloidal NRs into structures with increased optical anisotropy, and (2) the macroscopic ordering of NR assemblies along the direction of the applied AC field. By modeling the alignment of NR ensembles using directional statistics, we experimentally quantify the maximum degree of order in terms of the average deviation angle relative to the field axis. Results show a consistent improvement in alignment as a function of NR concentration—with a minimum average deviation of 18.7°—indicating that mesoscale assembly helps facilitate field-driven alignment of colloidal NRs.
Medium and Large N-Heterocycle Formation via Allene Hydroami-nation with a Bimetallic Rh(I) Catalyst
Authors: Forson Kelton , Bohman Benjamin , Wayment Coriantumr , Owens Rachel , McKnight Caitlyn , Davis Rhen , Stillwell Lillian , Michaelis David
Published: February 2022

We report the synthesis of a bimetallic Rh(I) complex containing a bridging CO ligand that facilitates Rh–Rh bond formation. This bimetallic complex enables intramolecular allene hydroamination to form seven to ten-member rings in high yield. Monometallic Rh complexes, in contrast, fail to achieve any product formation. We demonstrate a broad substrate scope for formation of a variety of N-heterocycles in good to excellent yields. Macrocyclization reactions that form eleven to fifteen-membered heterocycles are also demonstrated. Mechanistic studies show that the reaction likely proceeds via catalyst protonation by trifluoroacetic acid, followed by reversible allene insertion and C–N bond-forming reductive elimination. The difference in product selectivity observed with our bimetallic catalyst vs monometallic Rh complexes may result from cooperativity between the two metals.
Exploration of the chemical space of DNA-encoded libraries
Authors: Zabolotna Yuliana , Pikalyova Regina , Volochnyuk Dmitriy , Horvath Dragos , Marcou Gilles , Varnek Alexandre
Published: February 2022

DNA-Encoded Library (DEL) technology has emerged as an alternative method for bioactive molecule discovery in medicinal chemistry. It enables simple synthesis and screening of compound libraries of enormous size. Even though it gains more and more popularity each day, there are almost no reports of chemoinformatics analysis of DEL chemical space. Therefore, in this project we aimed to generate and analyze theultra-large chemical space of DEL. Around 2500 DELs were designed using commercially available BBs resulting in 2,5B DEL compounds that were compared to biologically relevant compounds from ChEMBL using Generative Topographic Mapping. This allowed to choose several optimal DELs covering the chemical space of ChEMBL to the highest extent and thus containing the maximum possible percentage of biologically relevant chemotypes. Different combinations of DELs were also analyzed to identify a set of mutually complementary libraries allowing to attain even higher coverage of ChEMBL than it is possible with one single DEL.
Solar-thermal production of graphitic carbon and hydrogen via methane decomposition
Authors: Abuseada Mostafa , Wei Chuyu , Spearrin R. Mitchell , Fisher Timothy S.
Published: February 2022

This work reports a process in which concentrated irradiation from a simulated solar source converts methane to high-value graphitic carbon and hydrogen gas. Methane flows within a photo-thermal reactor through the pores of a thin substrate irradiated by several thousand suns at the focal peak. The methane decomposes primarily into hydrogen while depositing highly graphitic carbon that grows conformally over ligaments in the porous substrate. The localized solar heating of the porous substrate serves to capture the solid carbon into a readily extractable and useful form while maintaining active deposition site density with persistent catalytic activity. Results indicate a strong temperature dependence with high decomposition occurring in the central heating zone with concentration factors and temperatures above 1000 suns and 1300 K, respectively. Even with a large flow area through regions of lower irradiation and temperature, methane conversion and hydrogen yields of approx. 70\% are achieved, and 58\% of the inlet carbon is captured in graphitic form.
How much can novel solid sorbents reduce the cost of post-combustion CO2 capture? A techno-economic investigation on the cost limits of pressure-vacuum swing adsorption
Authors: Subraveti Sai Gokul , Roussanaly Simon , Anantharaman Rahul , Riboldi Luca , Rajendran Arvind
Published: February 2022

This paper focuses on identifying the cost limits of two single-stage pressure-vacuum swing adsorption (PVSA) cycles for post-combustion CO2 capture if the ``ideal'' zero-cost adsorbent can be discovered. Through an integrated techno-economic optimisation, we simultaneously optimise the adsorbent properties (adsorption isotherms and particle morphology) and process design variables to determine the lowest possible cost of CO2 avoided (excluding the CO2 conditioning, transport and storage) for different industrial flue gas CO2 compositions and flow rates. The CO2 avoided cost for PVSA ranges from 87.1 to 10.4 € per tonne of CO2 avoided, corresponding to CO2 feed compositions of 3.5 mol% to 30 mol%, respectively. The corresponding costs for a monoethanolamine based absorption process, using heat from a natural gas plant, are 76.7 and 54.8 € per tonne of CO2 avoided, respectively, showing that PVSA can be attractive for flue gas streams with high CO2 compositions. The ``ideal" adsorbents needed to attain the lowest possible CO2 avoided costs have a range of CO2 affinities with close to zero N2 adsorption, demonstrating promise for adsorbent discovery and development. The need for simultaneously optimizing the particle morphology and the process conditions are emphasized.
Remarkable Enhancement of Catalytic Activity of Cu-Complexes in the Electrochemical Hydrogen Evolution Reaction (HER) by Using Triply-Fused Porphyrin
Authors: Sarkar Biprajit , Chandra Shubhadeep , Singha Hazari Arijit , Song Qian , Hunger David , Neuman Nicolas I. , van Slageren Joris , Klemm Elias
Published: February 2022

Developing efficient molecular catalysts for the electrocatalytic hydrogen evolution reaction (HER) is a highly important goal in contemporary science. We report here on a bimetallic triply fused copper porphyrin complex (1) comprising two monomeric porphyrin units linked through β–β, meso–meso, β′–β′ triple covalent linkages, that exhibits remarkable enhancement of catalytic activity for the electrochemical HER in comparison to the analogous monomeric copper porphyrin complex (2). Spectroscopic characterization, in association with magnetic measurements, clearly establish the ground state structures of both the bimetallic and monometallic complexes as containing two and one copper (II) centers, respectively. The fused metalloporphyrin complex is found to undergo electrochemical reduction at a lower negative applied potential compared to the metalloporphyrin monomer, as evident from the significant anodic shift (~800mV) in the potential of the first reduction process. Electrochemical investigations in the presence of a proton source (trifluoroacetic acid) confirm that the catalytic activity of the fused metalloporphyrin occurs at a significantly lower onset potential, (overpotential decreased by ~320 mV), compared to the non-fused monomer. Controlled potential electrolysis combined with the kinetic analysis of catalysts 1 and 2 confirm the production of hydrogen, with 96% and 71% faradaic efficiencies and turnover numbers of 102 and 18, respectively. Kinetic investigations further reveal an observed rate constant of around 107 (s-1), implying high efficiency of the bimetallic catalyst towards hydrogen evolution reaction. Mechanistic insights are presented by using a combination of UV-vis-NIR and EPR spectroscopy and electrochemistry. Our results thus firmly establish the triply fused porphyrin ligands as candidates for generating highly efficient molecular electrocatalysts in combination with transition metal centers.
Unusually Strong Long-range Electronic Coupling Across Redox-Active Bridges in M3+/M4+ Mixed-Valence Complexes of Group 4 Congeners
Authors: Bell Colby Seth , DeYonker Nathan J. , Moore Curtis E. , Clark Kensha Marie
Published: February 2022

Homobimetallic complexes of Group 4 metals, supported by the redox-active tetrakis(imino)pyracene (TIP) ligand were synthesized and isolated. The formation of these complexes resulted in LUMOs having significantly lower energies than the free ligand and the respective metal salts, MCl4 (M = Ti, Zr, Hf), whereby all three complexes were readily reduced by one electron using the mild reductant, Cp*2Fe (E0 = -0.59 V). Spectroscopic characterization and quantum chemical analyses of the reduced species revealed that the resulting complexes are delocalized, borderline Class II-III (Ti) and Class III (Zr, Hf) mixed valence complexes. All three complexes display surprisingly strong long-range electronic coupling between the metal centers, as M to M distances, rAB, are nearly 12 Å. The coupling strengths of Zr and Hf were significantly stronger than those observed for the Ti complex, suggesting that better orbital overlap between the ligand and 4d or 5d metal centers helps to relieve the instability of the 3+ oxidation state via delocalization.
ICP-MS Analysis of Mercury in Fish: Exploration of Method Validation, Matrix Effect, and Kinetic Energy Discrimination
Authors: Jung Wonhyeuk , Dunham Christopher , Perrotta Katie , Chen Yu , Gimzewski James , Loo Joseph
Published: February 2022

Inductively coupled plasma-mass spectrometry (ICP-MS) is a powerful analytical technique that can quantify elements of interest at parts-per-trillion concentrations. In this laboratory class, students performed ICP-MS analysis to quantify mercury concentration of standard reference material (SRM) 1947 (Lake Michigan fish tissue) and canned tuna from a local supermarket. These two samples were digested in two different matrices (HNO3/ H2O2 or HNO3/HCl/H2O2) and then analyzed using no-gas mode or helium mode with two different kinetic energy discrimination voltages (2V or 4V). The inclusion of HCl in the matrix produced more accurate results and stabilized mercury over the 8-day period after the digestion. Based on their analysis, the students were asked to draw their own conclusions about what they perceived to be the most accurate representation of the true mercury concentration of the tuna samples. This laboratory class provides students with a wide range of scientific concepts to explore such as method verification with SRM, kinetic energy discrimination, matrix effect, and trace metal stability over time.
Studies on the Synthesis of Perfluoroaryl Sulfides and their Application in Desulfurative Nickel-Catalyzed Reductive Cross-Coupling
Authors: Lee Shao-Chi , Hsu Che-Ming , Kao Hsin , Li Li-Yun , Tsai Zong-Nan , Tsao Yong-Ting , Hsu Yu-Ling , Miñoza Shinje , Chiu Cheng-chau , Liao Hsuan-Hung
Published: February 2022

The C−S activation and sulfur removal from native thiols is challenging and limits the application of thiols as typical feedstock materials in organic synthesis despite their natural abundance. Herein, we describe a simple procedure to introduce a per-/polyfluoroaryl moiety, which serves as a redox-active scaffold, into alkyl/aryl thiols using nucleophilic aromatic substitution (SNAr) chemistry to activate the C−S bond. The per-/polyfluoroaryl group acts as an electron acceptor in single electron transfer events to generate radical intermediates through cleavage of the C−S bond of mercaptans and utilize them in nickel-catalyzed reductive cross-coupling reactions. In addition, using computational methods, we shed light on the mechanism of this class of SNAr reaction and show that the preference for a concerted or stepwise mechanistic pathway can be easily rationalized through a Marcus-type argument, as well as consideration of the relative stability of the potential energy surfaces.
Hydrophobic surface patterning with soft, wax-infused micro-stamps
Authors: Torabi Soroosh , Cai Zhuoyun , Pham Jonathan , Trinkle Christine
Published: February 2022

In this paper, we demonstrate an easy-to-use and inexpensive stamping method that can be used to generate hydrophobic paraffin surface patterns on a variety of materials and surface geometries, including flat and curved surfaces. In this method, a waxy Parafilm sheet is placed on the back of a polydimethylsiloxane (PDMS) stamp containing microscale surface features; when heated above the melting temperature, the paraffin liquefies and diffuses into the stamp, which functions as a paraffin reservoir. The directional diffusion of the paraffin allows only a thin layer of liquid to be present at the micropatterned stamp surface. Hence, when it is put into contact with a target surface, it transfers a paraffin pattern with submicron lateral resolution and sub-100 nm thickness. By using XPS analysis to track paraffin diffusion process within the PDMS stamp, the diffusion coefficient in PDMS is estimated to be 5.3 x 10-11 m2/s at 65°C. In addition to improved patterning, the paraffin-saturated PDMS stamp removes the need for re-inking for consecutive patterning. In general, our process allows for rapid deposition of complex, multi-layer paraffin patterns on a variety of surfaces.
Insights into the Binding and Covalent Inhibition Mechanism of PF-07321332 to SARS-CoV-2 Mpro
Authors: Ngo Son Tung , Nguyen Trung Hai , Tung Nguyen Thanh , Mai Binh Khanh
Published: February 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic resulting in several million death were reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 is currently under clinical trial for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 µs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. Successfully generated bound state between two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of thioimidate product from SARS-CoV-2 Mpro and PF07321332 inhibitor. We found that the catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays important role in the activation of PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for better understanding on the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro.
Porphyrin based metal-organic frameworks with record sensitivity in optical oxygen sensing
Authors: Burger Tobias , Winkler Christian , Dalfen Irene , Slugovc Christian , Borisov Sergey
Published: February 2022

The optical oxygen sensing capabilities of the porphyrin-based metal-organic frameworks, PCN-224, Pt(II)PCN-224 and Pd(II)PCN-224 were investigated. The bimolecular quenching constants (kq) of 37000 (PCN-224), 6700 (Pd(II)PCN-224) and 3900 Pa-1s-1 (Pt(II)PCN-224) were found and reveal an exceptionally high oxygen-permeability for these materials. A fast gas transport within the network, large pore sizes, electronic and spatial isolation of the porphyrin indicator in the framework are held responsible for the unprecedentedly high kq values. PCN-224 shows 6.7 ns fluorescence lifetime and the fluorescence in air is quenched by 4.2-fold. The metal-organic frameworks based on phosphorescent Pt(II) and Pd(II) porphyrins possess significantly longer decay times of 18.6 and 390 µs, respectively, and are suited to detect oxygen in trace and ultra-trace ranges with limits of detection of 1 and 0.015 Pa, respectively. Apart from free-standing crystals, also metal-organic frameworks supported on different fibrous substrates (poly(acrylonitrile) nanofibers, glass fibres), and flat substrates (TLC silica-gel, poly(amide) filter) were prepared in order to provide oxygen sensor materials of practical use. Electrospun and thermally treated poly(acrylonitrile) nanofibers were proven to be particularly favourable and the resulting composite material exhibited the same sensitivity as the free crystals. All sensing materials show reversible cross-talk to humidity at levels up to 53 % relative humidity but demonstrate a drastic decrease of oxygen sensitivity at high humidity levels and when exposed to water.
Machine Learning of Reaction Properties via Learned Representations of the Condensed Graph of Reaction
Authors: Heid Esther , Green William H.
Published: February 2022

The estimation of chemical reaction properties such as activation energies, rates or yields is a central topic of computational chemistry. In contrast to molecular properties, where machine learning approaches such as graph convolutional neural networks (GCNNs) have excelled for a wide variety of tasks, no general and transferable adaptations of GCNNs for reactions have been developed yet. We therefore combined a popular cheminformatics reaction representation, the so-called condensed graph of reaction (CGR), with a recent GCNN architecture to arrive at a versatile, robust and compact deep learning model. The CGR is a superposition of the reactant and product graphs of a chemical reaction, and thus an ideal input for graph-based machine learning approaches. The model learns to create a data-driven, task dependent reaction embedding that does not rely on expert knowledge, similar to current molecular GCNNs. Our approach outperforms current state-of-the-art models in accuracy, is applicable even to imbalanced reactions and possesses excellent predictive capabilities for diverse target properties, such as activation energies, reaction enthalpies, rate constants, yields or reaction classes. We furthermore curated a large set of atom-mapped reactions along with their target properties, which can serve as benchmark datasets for future work. All datasets and the developed reaction GCNN model are available online, free of charge and open-source.
Atomistic Nodal Approach: a General Molecular Dynamics Method For Computing Local Thermal Conductance at Atomistic Resolution
Authors: Jiang Mingxuan , Olarte-Plata Juan D. , Bresme Fernando
Published: February 2022

The Interfacial Thermal Conductance (ITC) is a fundamental property of mate- rials and has particular relevance at the nanoscale. The ITC quanti�es the thermal resistance between materials of dierent compositions or between uids in contact with materials. Furthermore, the ITC determines the rate of cooling/heating of the materi- als and the temperature drop across the interface. Here we propose a method to com- pute local ITCs and temperature drops of nanoparticle- uid interfaces. Our approach resolves the ITC at the atomic level using the atomic coordinates of the nanomaterial as nodes to compute local thermal transport properties. We obtain high-resolution descriptions of the interfacial thermal transport by combining the atomistic nodal ap- proach, computational geometry techniques and \computational farming" using Non- Equilibrium Molecular Dynamics simulations. We illustrate our method by analyzing various nanoparticles as a function of their size and geometry, targeting experimentally relevant structures like capped octagonal rods, cuboctahedrons, decahedrons, rhombic dodecahedrons, cubes, icosahedrons, truncated octahedrons, octahedrons and spheres. We show that the ITC of these very dierent geometries can be accurately described in terms of the local coordination number of the atoms in the nanoparticle surface. Nanoparticle geometries with lower surface coordination numbers feature higher ITCs, and the ITC generally increases with decreasing particle size.
Truly Random Degradable Vinyl Copolymers via Photocontrolled Radical Ring-Opening Cascade Copolymerization
Authors: Wang Wenqi , Zhou Zefeng , Tang Xuanting , Moran Stephanie , Jin Jing , Haeffner Fredrik , Niu Jia
Published: February 2022

Degradable vinyl polymers by radical ring-opening polymerization have become a promising solution to the challenges caused by the widespread use of non-degradable vinyl plastics. However, achieving even distribution of labile functional groups in the backbone of degradable vinyl polymers remains challenging. Herein, we report a photocatalytic approach to truly random degradable vinyl copolymers with tunable main-chain composition via radical ring-opening cascade copolymerization (rROCCP). The rROCCP of the macrocyclic allylic sulfone and acrylates or acrylamides mediated by visible light at ambient temperature achieved near-unity reactivity ratios of both comonomers over the entire range of the comonomer compositions and afforded truly random vinyl copolymers with degradable units evenly distributed in the polymer backbone. Experimental and computational evidence revealed an unusual reversible inhibition of chain propagation by in situ generated sulfur dioxide, which was successfully overcome by reducing the solubility of sulfur dioxide in the reaction mixture. This study provided a powerful approach to truly random degradable vinyl copolymers with tunable main-chain labile functionalities and comparable thermal and mechanical properties to traditional non-degradable vinyl polymers.
Mechanistic insights into pH-dependent hydrogen electrocatalysis by flipping interfacial water
Authors: Sun Qiang , Oliveira Nicholas , Tyukhtenko Sergiy , Guo Jason , Myrthil Nathalie , Lopez Steven , Kendrick Ian , Mukerjee Sanjeev , Ma Lu , Ehrlich Steven , Li Jingkun , Yan Yushan , Jia Qingying
Published: February 2022

A grand challenge in electrochemistry is to understand and promote electrochemical processes by exploring and exploiting the interface. Herein, we promoted the hydrogen evolution and oxidation reactions (HER/HOR) of platinum in base by employing N-methylimidazoles to reorientate interfacial water against the interfacial electric field as evidenced by in situ spectroscopic characterization of the interface. We accordingly established a unified mechanism by which the HER/HOR in acid and base proceeds via diffusion of proton and hydroxide, respectively, through interface via interfacial water by the Grotthuss mechanism. This mechanism accounts for the pH-dependent HER/HOR kinetics of platinum, a long-standing puzzle. Furthermore, we demonstrated 40% performance improvement of an anion exchange membrane electrolyzer by adding 1,2-dimethylimidazole into the alkaline solution fed into its Pt cathode.