bluuebunny/crossref_metadata_2025 huggingface dataset:
Confined Pulsed Diffuse Layer Charging for Nanoscale Electrodeposition with an STM
Authors: Aarts Mark , Reiser Alain , Spolenak Ralph , Alarcon-Llado Esther
Published: February 2022

Regulating the state of the solid-liquid interface by means of electric fields is a powerful tool to control electrochemistry. In scanning probe systems, this can be confined closely to a scanning (nano)electrode by means of fast potential pulses, providing a way to probe the interface and control electrochemical reactions locally, as has been demonstrated in nanoscale electrochemical etching. For this purpose, it is important to know the spatial extent of the interaction between pulses applied to the tip, and the substrate. In this paper we use a framework of diffuse layer charging to describe the localization of electrical double layer charging in response to a potential pulse at the probe. Our findings are in good agreement to literature values obtained in electrochemical etching. We show that the pulse can be much more localized by limiting the diffusivity of the ions present in solution, by confined electrodeposition of cobalt in a dimethyl sulfoxide solution, using an electrochemical scanning tunneling microscope. Finally, we demonstrate the deposition of cobalt nanostructures (<100 nm) using this method. The presented framework therefore provides a general route for predicting and controlling the time-dependent region of interaction between an electrochemical scanning probe and the surface.
Genetic Encoding of Cyanopyridylalanine for In-Cell Protein Macrocyclization by the Nitrile-Aminothiol Click Reaction
Authors: Abdelkader Elwy , Qianzhu Haocheng , George Josemon , Frkic Rebecca , Jackson Colin , Nitsche Christoph , Otting Gottfried , Huber Thomas
Published: February 2022

Cyanopyridylalanines are non-canonical amino acids that react with aminothiol compounds under physiological conditions in a biocompatible manner without requiring added catalyst. Here we present newly developed aminoacyl-tRNA synthetases for genetic encoding of meta- and para-cyanopyridylalanine to enable the site-specific attachment of a wide range of different functionalities. The outstanding utility of the cyanopyridine moiety is demonstrated by examples of (i) post-translational functionalization of proteins, (ii) in-cell macrocyclization of peptides and proteins, and (iii) protein stapling. The biocompatible nature of the protein ligation chemistry enabled by the cyanopyridylalanine amino acid opens a new path to specific in vivo protein modifications in complex biological environments.
Surface Stability and Morphology of Calcium Phosphate Tuned by pH Values and Lactic Acid Additives: Theoretical and Experimental Study
Authors: Chen Hongwei , Lv Changchang , Guo Lin , Ma Ming , Li Xiangfeng , Lan Zhengyi , Huo Jun , Dong Hao , Zhu Xiangdong , Zhu Qiang , Gu Yuming , Liu Ziteng , Liu Jianjun , Chen Hangrong , Guo Xuefeng , Ma Jing
Published: February 2022

The ubiquitous mineralization of calcium phosphate (CaP) facilitates biological organisms to produce hierarchically structured minerals. The coordination number and strength of Ca2+ ions with phosphate species, oxygen-containing additives, and solvent molecules played a crucial role in tuning nucleation processes and surface stability of CaP under the simulated body fluid (SBF) or aqueous solutions upon the addition of oligomeric lactic acid (LACn, n=1, 8) and changing pH values. As revealed by ab initio molecular dynamics (AIMD), density functional theory (DFT), and molecular dynamics (MD) simulations as well as high-throughput experimentation (HTE), the binding of LAC molecules with Ca2+ ions and phosphate species could stabilize both pre-nucleation clusters and brushite (DCPD, CaHPO4·2H2O) surface through intermolecular electrostatic and hydrogen bonding interactions. When the concentration of Ca2+ ions ([Ca2+]) is very low, the amount of the formed precipitation decreased with the addition of LAC based on UV-Vis spectroscopic analysis due to the reduced chance for the LAC capped Ca2+ ions to coordinate with phosphates and the increased solubility in acid solution. With the increasing [Ca2+] concentration, the kinetically stable DCPD precipitation was obtained with high Ca2+ coordination number and low surface energy. Morphologies of DCPD precipitation are in plate, needle, or rod, depending on the initial pH values that tuned by adding NH3·H2O, HCl, or CH3COOH. The prepared samples at pH ≈ 7.4 with different Ca/P ratios exhibited negative zeta potential values, which were correlated with the surface electrostatic potential distributions and potential biological applications.
Unified Template Strategy for Editing Multiple Remote C–H Bonds
Authors: Fan Zhoulong , Chen Xiangyang , Tanaka Keita , Park Han Seul , Lam Nelson Y. S. , Wong Jonathan J. , Houk K. N. , Yu Jin-Quan
Published: February 2022

Through consecutive selective C–H functionalization at multiple sites, the direct molecular editing of heteroarene carbon-hydrogen (C–H) bonds has the potential to grant rapid access into diverse molecular space; a valuable but often challenging venture to achieve in medicinal chemistry. Contrasting with electronically-biased heterocyclic C–H bonds, remote benzocyclic C–H bonds on bicyclic aza-arenes are especially difficult to differentiate due to lack of intrinsic steric/electronic biases. Through careful consideration of distance and geometric parameters, we herein report a unified catalytic directing template strategy that enables the modular functionalization of chemically-similar and adjacent remote positions on bicyclic aza-arene scaffolds. Differentiated by using two structurally distinct catalytic directing templates, this method enables direct C–H olefination, alkynylation, and allylation at previously inaccessible C6 and C7 positions of quinolines, and is amenable to the iterative, modular, and late-stage C–H editing of quinoline-containing pharmacophores and pharmaceuticals. This report, in combination with our previous C5-selective template and other complementary methods, now fully establishes a unified ‘molecular editing’ strategy to directly modify aza-arene heterocycles at any given site.
Relaxation Time Correlation NMR for Mechanochemical in-situ Reaction Monitoring of Metal-Organic Frameworks
Authors: Leger Madeleine , Guo Jiangfeng , MacMillan Bryce , Titi Hatem , Friscic Tomislav , Blight Barry , Balcom Bruce
Published: February 2022

We present a new methodology for real-time observation of mechanochemical transformations, based on a magnetic resonance method in which T1-T2* relaxation time correlation maps are used to track the formation of the popular metal-organic framework (MOF) materials Zn-MOF-74 and ZIF-8. This two-dimensional (2D) relaxation correlation measurement is a new method utilizing simple saturation recovery to obtain a T1-T2* spectrum representing different hydrogen environments. The 2D T1-T2* results show a change in signal amplitudes, and their coordinates, within the plots as the reaction progresses, confirming reaction completion. Static solid samples are usually considered difficult to measure because of their short-lived T2* signal and their common non-exponential decay. Using a new processing method, the signal from samples with non-exponential decay was quantified. The importance of key parameters such as the instrument deadtime, the recovery times, and magnetic field strength for the measurement of solids with a short-lived signal is established. This novel magnetic resonance measurement is important since it provides a simple and easy way to analyse an entire solid reaction mixture within its reaction vessel.
Insights Into the Uptake of N2O5 by Aqueous Aerosol Using Chemically Accurate Many-Body Potentials
Authors: Cruzeiro Vinicius Wilian D. , Galib Mirza , Limmer David T. , Goetz Andreas W.
Published: February 2022

We study the uptake of N2O5 into pure water using molecular dynamics simulations performed with a recently developed, data driven MB-nrg model. Our model follows the same basis of the MB-pol water many body model and has coupled-cluster accuracy. We quantify the thermodynamics of solvation and adsorption using enhanced sampling techniques and free energy calculations. The free energy profile obtained highlights that N2O5 is selectively adsorbed to the liquid-vapor interface and weakly solvated. We further find that accommodation into the bulk solution occurs rather slowly, and competes with evaporation upon initial adsorption from the gas phase. The rates of each of these processes are evaluated using the free energy barriers and kinetically obtained fluxes. Leveraging the quantitative accuracy of the model, we parameterize and numerically solve a reaction-diffusion equation to determine a likely range of hydrolysis rates consistent with the experimentally observed reactive uptake coefficient in pure water. The physical and chemical parameters deduced here, including the solubility, accommodation coefficient, and hydrolysis rate, afford a foundation for which to consider the reactive loss of N2O5 in more complex solutions.
Construction of vicinal 4°/3°-carbons via reductive Cope rearrangement
Authors: Sobie Kristin , Albritton Matthew , Yang Yinuo , Alves Mariana , Roitberg Adrian , Grenning Alexander
Published: February 2022

Herein reported is a strategy for constructing vicinal 4°/3° carbons via reductive Cope rearrangement. Substrates have been designed which exhibit Cope rearrangement kinetic barriers in the range of ~23 kcal/mol with isothermic favorability (G ~0). These fluxional/shape-shifting molecules can be driven forward by chemoselective reduction to useful polyfunctionalized building blocks.
First-row Transition Metal Antimonates for the Oxygen Reduction Reaction
Authors: Gunasooriya G. T. Kasun Kalhara , Kreider Melissa E. , Liu Yunzhi , Zamora Zeledón José A. , Wang Zhenbin , Valle Eduardo , Yang An-Chih , Gallo Alessandro , Sinclair Robert , Burke Stevens Michaela , Jaramillo Thomas F. , Nørskov Jens K.
Published: February 2022

The development of inexpensive and abundant catalysts with high activity, selectivity, and stability for the oxygen reduction reaction (ORR) is imperative for the widespread implementation of fuel cell devices. Herein, we present a combined theoretical-experimental approach to discover and design first-row transition metal antimonates as promising electrocatalytic materials for the ORR. Theoretically, we identify first-row transition metal antimonates – MSb2O6, where M = Mn, Fe, Co, and Ni – as non-precious metal catalysts with promising oxygen binding energetics, conductivity, thermodynamic phase stability and aqueous stability. Among the considered antimonates, MnSb2O6 shows the highest theoretical ORR activity based on the 4e− ORR kinetic volcano. Experimentally, nanoparticulate transition metal antimonate catalysts are found to have a minimum of a 2.5-fold enhancement in intrinsic mass activity (on transition metal mass basis) relative to the corresponding transition metal oxide at 0.7 V vs RHE in 0.1 M KOH. MnSb2O6 is the most active catalyst under these conditions, with a 3.5-fold enhancement on a per Mn mass activity basis and 25-fold enhancement on a surface area basis over its antimony-free counterpart. Electrocatalytic and material stability are demonstrated over a 5 h chronopotentiometry experiment in the stability window identified by Pourbaix analysis. This study further highlights the stable and electrically conductive antimonate structure as a promising framework to tune the activity and selectivity of non-precious metal oxide active sites for ORR catalysis.
Electrochemical and Molecular Assessment of Quinones as CO2-Binding Redox Molecules for Carbon Capture
Authors: Simeon Fritz , Stern Michael C. , Diederichsen Kyle M. , Liu Yayuan , Herzog Howard J. , Hatton T. Alan
Published: February 2022

The complexation and decomplexation of CO2 with a series of quinones of different basicity during electrochemical cycling in dimethylformamide solutions were studied systematically by cyclic voltammetry. In the absence of CO2, all quinones exhibited two well-separated reduction waves. For weakly complexing quinones, a positive shift in the second reduction wave was observed in the presence of CO2, corresponding to the dianion quinone-CO2 complex formation. The peak position and peak height of the first re-duction wave were unchanged, indicating no formation of complexes between the semiquinones and CO2. The relative heights of both reduction waves remained constant. In the case of strongly complexing quinones, the second reduction wave disappeared while the peak height of the first reduction wave approximately doubled, indicating that the two electrons transferred simultaneously at this potential. The observed voltammograms were rationalized through several equilibrium arguments. Both weakly and strongly complexing quinones underwent either stepwise or concerted mechanisms of oxidation and CO2 dissociation depending on the sweep rate in the cyclic voltammetric experiments. Relative to stepwise oxidation, the concerted process requires a more positive electrode potential to remove the electron from the carbonate complexes to release CO2 and regenerate the quinone. For weakly complexing quinones, the stepwise process corresponds to oxidation of the uncomplexed dianion and accompanying equilibrium shift, while for strongly complexing quinones the stepwise process would correspond to the oxidation of mono(carbonate) dianion to the complexed semiquinone and accompanying equilibrium shift. This study provides a mechanistic interpretation of the interactions that lead to the formation of quinone-CO2 complexes required for the potential development of an energy efficient electrochemical separation process and discusses important considerations for practical implementation of CO2 capture in the presence of oxygen with lower vapor pressure solvents.
Dehydration Enhances Prebiotic Lipid Remodeling and Vesicle Formation in Acidic Environments
Authors: Steller Luke H , Van Kranendonk Martin J , Wang Anna
Published: February 2022

The encapsulation of genetic polymers inside lipid bilayer compartments is a vital step in the emergence of cell-based life. However, even though acidic conditions promote many reactions required for generating prebiotic building blocks, prebiotically-relevant lipids tend to form denser aggregates at acidic pHs rather than prebiotically useful vesicles that exhibit sufficient solute encapsulation. Here we describe how dehydration/rehydration (DR) events, a prebiotically-relevant physicochemical process known to promote polymerization reactions, can remodel dense lipid aggregates into thin-walled vesicles capable of RNA encapsulation even at acidic pHs. Furthermore, DR events appears to favor the encapsulation of RNA within thin-walled vesicles over more lipid-rich vesicles, thus conferring such vesicles a selective advantage.
3D-printed hierarchical pillar array electrodes for high performance semi-artificial photosynthesis
Authors: Zhang Jenny , Chen Xiaolong , Lawrence Joshua , Wey Laura , Jing Qingshen , Kar-Narayan Sohini , Schertel Lukas , Vignolini Silvia , Howe Christopher
Published: February 2022

The re-wiring of photosynthetic bio-machineries to electrodes is a forward-looking semi-artificial route for sustainable bio-electricity and fuel generation. Currently, it is unclear how the bio-material interface can be designed to meet the complex requirements for high bio-photoelectrochemical performance. Here, we developed an aerosol jet printing method for generating hierarchical electrode structures using indium tin oxide nanoparticles. We printed libraries of micropillar array electrodes varying in height and sub-micron surface features and studied the energy/electron transfer processes across the bio-electrode interfaces. When wired to the cyanobacterium Synechocysis sp. PCC 6803, micropillar array electrodes with micro-branches gave rise to substantially enhanced biocatalyst loading, light input, and electron flux output compared to state-of-the-art porous structures of the same height. Micropillar electrodes 600 µm in height reached milestone mediated photocurrent densities of 245 µA cm–2 (the closest thus far to theoretical predictions) and external quantum efficiencies of up to 29%. This study provides a blueprint for bio-hybrid electrode design, and tools for where electrode architecture is vital for performance.
A Convenient Synthesis of Thiol, Trithiocarbonate and Disulfide
Authors: Gondi Sudershan Reddy , Rissing Christiana Julia , SON DAVID
Published: February 2022

Synthesis of unsymmetrical trithiocarbonate sulfonate salt, along with disulfide, thiol andsymmetrical trithiocarbonate from 3-mercapto-1-propane-sulfonicacid, sodium salt with, withoutof phase transfer catalyst and under various reaction conditions are described. The obtainedcompounds having divergent usefulness in RAFT polymerization, sulfonyl preparation andhaving capable of binding in a multidentate fashion to soft transition metal ions.
Nanoparticle–Size–Dependent Singlet Fission and Exciton Dynamics in Amorphous TIPS-Pentacene
Authors: Hudson Rohan , Stuart Alexandra , de la Perrelle Jessica , Huang David , Kee Tak W.
Published: February 2022

Aqueous nanoparticle (NP) dispersions are commonly used as model systems for spectro- scopic study of singlet exciton fission (SF) in acenes such as 6,13-(triisopropylsilylethynyl) pentacene (TIPS-Pn). However, the potential for particle size effects to complicate interpretation of results in such model systems is generally ignored. In this work, we study amorphous TIPS-Pn NP dispersions prepared by the re-precipitation method over a range of particle sizes. Time-resolved fluorescence and femtosecond transient absorption spectroscopy show that exciton dynamics in these systems depend significantly upon particle size. Kinetic analysis reveals that SF becomes slower at smaller NP sizes, while triplet exciton decay (through both correlated triplet pair relaxation and geminate triplet-triplet annihilation) accelerates. These significant size-dependent effects are ascribed to increased morphological disorder within smaller NPs, weakening the intermolecular couplings which control SF and triplet migration. A non-radiative singlet quenching channel separate from SF is also identified, which has not been previously reported for NPs of SF-capable chromophores. This non-radiative singlet decay becomes a significant relaxation pathway at small particle sizes, substantially reducing SF yields. Interestingly, exciton kinetics in 81-nm NPs approach those of bulk amorphous TIPS-Pn, suggesting that NPs of this size or larger are likely good models for bulk TIPS-Pn. This work demonstrates that particle-size effects are significant for small NPs of SF chromophores, and must be accounted for in order to accurately model bulk materials with such NP dispersions.
Umpolung Strategy for Arene C–H Etherification Leading to Functionalized Chromanes Enabled by I(III) N-Ligated Hypervalent Iodine Reagents
Authors: Mikhael Myriam , Guo Wentao , Tantillo Dean J. , Wengryniuk Sarah E.
Published: February 2022

The direct formation of aryl C–O bonds via the intramolecular dehydrogenative coupling of a C–H bond and a pendant alcohol represents a powerful synthetic transformation. Herein, we report a method for intramolecular arene C–H etherification via an umpoled alcohol cyclization mediated by an I(III) N-HVI reagent. This approach provides access to functionalized chromane scaffolds from primary, secondary and tertiary alcohols via a cascade cyclization-iodonium salt formation, the latter providing a versatile functional handle for downstream derivatization. Computational studies support initial formation of an umpoled O-intermediate via I(III) ligand exchange, followed by competitive direct and spirocyclization/1,2-shift pathways.
Divalent Ion-Specific Outcomes on Stern Layer Structure and Total Surface Potential at the Silica:Water Interface
Authors: Ma Emily , Geiger Franz
Published: February 2022

The second-order nonlinear susceptibility, chi(2), in the Stern layer, and the total interfacial potential drop, Phi(0)tot, across the oxide:water interface are estimated from SHG amplitude and phase measurements for divalent cations (Mg2+, Ca2+, Sr2+, Ba2+) at the silica:water interface at pH 5.8 and various ionic strengths. We find that interfacial structure and total potential depend strongly on ion valency. We observe statistically significant differences between the experimentally determined chi(2) value for NaCl and that of the alkali earth series, but smaller differences between ions of the same valency in that series. These differences are particularly pronounced at intermediate salt concentrations, which we attribute to the influence of hydration structure in the Stern layer. Furthermore, we corroborate the differences by examining the effects of anion substitution (SO4 2- for Cl-). Finally, we identify that hysteresis in measuring the reversibility of ion adsorption and desorption at fused silica in forward and reverse titrations manifests itself both in Stern layer structure and in total interfacial potential for some of the salts, most notable CaCl2 and MgSO4, but less so for BaCl2 and NaCl.
De novo Sequencing and Native Mass Spectrometry Reveals Hetero-Association of Dirigent Protein Homologs and Potential Interacting Proteins in Forsythia × intermedia
Authors: Zhou Mowei , Laureanti Joseph , Bell Callum , Kwon Mi , Meng Qingyan , Novikova Irina , Thomas Dennis , Nicora Carrie , Sontag Ryan , Bedgar Diana , O’Bryon Isabelle , Merkley Eric , Ginovska Bojana , Cort John , Davin Laurence , Lewis Norman
Published: February 2022

The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with Forsythia × intermedia. Stereo-selective, DP-guided, monolignol-derived radical coupling in vitro was then reported to afford the optically active lignan, (+)-pinoresinol from coniferyl alcohol, provided one-electron oxidase/oxidant capacity was present. It later became evident that DPs have several distinct sub-families. In vascular plants, DPs hypothetically function, along with other essential enzymes/proteins (e.g. oxidases), as part of lignin/lignan forming complexes (LFCs). Herein, we used an integrated bottom-up, top-down, and native mass spectrometry approach to detect potential interacting proteins in a DP-enriched solubilized protein fraction from Forsythia × intermedia, via adaptation of our initial report of DP solubilization and purification. Because this hybrid species lacks a published genome, de novo sequencing was performed using publicly available transcriptome and genomic data from closely related species. We detected and identified two new DP homologs, which appear to form hetero-trimers. Molecular dynamics simulations suggest that similar hetero-trimers were possible between Arabidopsis DP homologs with comparable sequence similarity. Other identified proteins in the DP-enriched preparation were putatively associated with DP function or the cell wall. Although their co-occurrence after extraction and chromatographic separation is suggestive for components of a protein complex in vivo, none were found to form stable complexes with DPs under the specific experimental conditions we have explored. Nevertheless, our integrated mass spectrometry method development helps prepare for future investigations directed to detect hypothetical LFCs and other related complexes isolated from plant biomass fractionation.
Modification of IL-6 by hypochlorous acid: effects on receptor binding and possible role in treatment of COVID-19
Authors: Robins Lori , Keim Erika , Robins Deborah , Edgar Scott , Meschke John , Gafken Philip , Williams Jeffrey
Published: February 2022

Interleukin-6 (IL-6) has been implicated in the pathogenesis of acute inflammatory events in COVID-19 patients. We exposed IL-6 to hypochlorous acid (HOCl) in vitro at concentrations reported to develop in vivo. After HOCl treatment the cytokine failed to bind to IL-6 receptors in a bioassay using engineered human cells. Similar results followed exposure of IL-6 to N-chlorotaurine (NCT) and hypobromous acid (HOBr). SDS-PAGE analysis of HOCl-treated IL-6 showed neither fragmentation nor aggregation, suggesting that the modifications induced by these agents occurred on the intact protein. Mass spectrometry of intact and trypsin-digested fragments identified oxidative changes limited to two amino acid residues, methionine 161 and tryptophan 157, both of which have been implicated in receptor binding of the cytokine. Further studies on the effects of hypohalous acids and their halogenated amine derivatives on IL-6 and related cytokines is needed.
Rearrangement of Thiodepsipeptides by S–N Acyl Shift Delivers Homodetic Autoinducing Peptides
Authors: Gless Bengt H. , Bejder Benjamin Svejdal , Monda Fabrizio , Bojer Martin S. , Ingmer Hanne , Olsen Christian Adam
Published: February 2022

Group behavior in many bacteria relies on chemically induced communication called quorum sensing (QS), which plays important roles in regulation of colonization, biofilm formation, and virulence. In Gram-positive bacteria, QS is often mediated by cyclic ribosomally synthesized and posttranslationally modified peptides (RiPPs). In staphylococci for example, most of these so-called autoinducing peptides (AIPs) contain a conserved thiolactone functionality, which has been predicted to constitute a structural feature of AIPs from other species as well. Here, we show that pentameric AIPs from Lactobacillus plantarum, Clostridium perfringens, and Listeria monocytogenes that were previously presumed to be thiolactone-containing structures readily rearrange to become homodetic cyclopeptides. This finding has implications for the developing understanding of the cross-species and cross-genus communication of bacteria and may help guide the discovery of peptide ligands to perturb their function.
Targeted positioning of quantum dots inside 3D silicon photonic crystals revealed by synchrotron X-ray fluorescence tomography
Authors: Schulz Andreas S. , Harteveld Cornelis A. M. , Vancso G. Julius , Huskens Jurriaan , Cloetens Peter , Vos Willem L.
Published: February 2022

It is a major outstanding goal in nanotechnology to precisely position functional nanoparticles, such as quantum dots, inside a three-dimensional (3D) nanostructure in order to realize novel functions. Once the 3D positioning is performed, the challenge arises how to non-destructively verify where the nanoparticles reside in the 3D nanostructure. Here, we study 3D photonic band gap crystals made of Si that are infiltrated with PbS nanocrystal quantum dots. The nanocrystals are covalently bonded to polymer brush layers that are grafted to the Si-air interfaces inside the 3D nanostructure using surface-initiated atom transfer radical polymerization (SI-ATRP). The functionalized 3D nanostructures are probed by synchrotron X-ray fluorescence (SXRF) tomography that is performed at 17 keV photon energy to obtain large penetration depths and efficient excitation of the elements of interest. Spatial projection maps were obtained followed by tomographic reconstruction to obtain the 3D atom density distribution with 50 nm voxel size for all chemical elements probed: Cl, Cr, Cu, Ga, Br, Pb. The quantum dots are found to be positioned inside the 3D nanostructure, and their positions correlate with the positions of elements characteristic of the polymer brush layer and the ATRP initiator. We conclude that X-ray fluorescence tomography is very well suited to non-destructively characterize 3D nanomaterials with photonic and other functionalities.
Structure of PtRu/Ru(0001) and AgPd/Pd(111) surface alloys: A kinetic Monte Carlo study
Authors: Mahlberg David , Sakong Sung , Gross Axel
Published: February 2022

Bimetallic surfaces allow tailoring their catalytic activity by modifying their composition and/or structure. However, under operating conditions, catalytically active bimetallic structures are often not stable and change their morphology which might reduce their functionality. Still, catalytically active structures do not necessarily need to be thermodynamically stable and might also be kinetically stabilized. Here we report kinetic Monte Carlo simulations based on density functional theory calculation to address the meta-stability of surface alloy systems. As structural changes can typically only occur via vacancy diffusion in the surface, we first determine the vacancy diffusion barrier as a function of their bimetallic environment. By determining the temporal evolution of the bimetallic surface alloys as a function of temperature, we analyze the factors underlying the stability and structure of the bimetallic surface alloys.
Pt(II)-Coordinated Tricomponent Self-Assemblies of Tetrapyridyl Porphyrin and Dicarboxylate Ligands: Are They 3D Prisms or 2D Bow Ties?
Authors: Benavides Paola , Gordillo Monica A. , Yadav Ashok , Joaqui-Joaqui M. Andrey , Saha Sourav
Published: February 2022

Thermodynamically favored heteroleptic coordination of Pt(II) ions with one aza- and another oxo-coordinating ligand yield tricomponent supramolecular coordination complexes (SCCs) that possess much greater structural complexity and functional diversity than traditional bicomponent SCCs containing only one ligand. Herein, we demonstrate that heteroleptic coordination of tetrapyridyl-porphyrins (MTPP, M = Zn or H2) and various dicarboxylate ligands (XDC) having different lengths and rigidity with cis-(Et3P)2PtII corners actually yields bow-tie (⋈)-shaped [{cis-(Et3P)2Pt}4(MTPP)(XDC)2]4+ complexes featuring a MTPP core and two parallel XDC linkers connected by four heteroligated PtII(N,O) corners. Although previous reports had claimed that the tricomponent self-assembly method produced tetragonal prisms having two cofacial MTPP and four XDC linkers connected by eight PtII(N,O) corners, our studies demonstrated that in reality, no such prism was formed, because instead of connecting two cofacial MTPP ligands, the XDC linkers actually bridged two adjacent pyridyl termini of an MTPP ligand via shared PtII(N,O) corners, forming bow-tie complexes.
Spreadability of Metal Powders for Laser-Powder Bed Fusion via Simple Image Processing Steps
Authors: Vakifahmetoglu Cekdar , Hasdemir Beyza
Published: February 2022

This paper investigates the spreadability of the spherical CoCrWMo powder for Laser- Powder Bed Fusion (PBF-LB) by using image processing algorithms coded in MATLAB. Besides, it also aims to examine the spreadability correlation with the other characteristics such as flow rate, apparent density, angle of repose. Powder blends in four different particle size distributions are prepared, characterized, and spreadability tests are performed with the PBF-LB. The results demonstrate that an increase in fine particle ratio by volume (below 10 µm) enhances the agglomeration and decreases the flowability, causing poor spreadability. These irregularities on the spread layers are quantified with simple illumination invariant analysis.
Catalytic Resonance Theory: Negative Dynamic Surfaces for Programmable Catalysts
Authors: Gathmann Sallye , Ardagh M. Alexander , Dauenhauer Paul
Published: February 2022

Catalysts that change with time via programmed variation of their electronic occupation to accelerate surface reactions were evaluated in the case of negative adsorption energy scaling relations. Defined as the relative change in adsorption enthalpy, the gamma linear scaling parameter is negative when two adsorbates alternatively weaken and strengthen as catalysts are electronically perturbed. Simulations were conducted of a single transition state connecting two generic adsorbates representative of multiple reaction classes to understand the resulting negative gamma catalytic ratchet mechanism and its ability to accelerate catalytic reactions above the Sabatier peak and away from equilibrium. Relative to conventional positive gamma catalytic ratchets, the Sabatier volcanoes of negative gamma catalysis are narrower with greater enhancement of dynamic turnover frequency when catalysts are electronically oscillated. Promotion of the catalytic surface reaction forwards or backwards was predictable by a descriptor accounting for the relative rates of forward and reverse kinetics under oscillatory conditions.
Mesoporous Silica with Covalently Immobilized Anthracene as Adsorbent for SPE Recovery of PAHs Pollutants from Highly Lipidic Solutions
Authors: Mikhraliieva Albina , Gonçalves Rodrigo Araújo , Zaitsev Volodymyr
Published: February 2022

Two samples of functionalized mesoporous silica containing anchored anthrylmethylamine groups (SiO2-Ant) have been prepared by surface assembling (1) and one step silane immobilization (2). Both adsorbents can be attributed to bimodal balanced hydrophobic-hydrophilic adsorbents with loading of anthracene groups about 15-33%. The adsorbents have been used for SPE of anthracene from organic solvents (acetonitrile, acetone and heptane) and model solutions of lipids (myristic acid and vegetable oil). The obtained results were compared with commercial C18 SPE cartridge. While C18 cartridge recovers anthracene from water-containing media (acetonitrile/water, 1/1), SiO2-Ant cartridges much more efficient in extraction of anthracene from non-polar solvent (heptane). Lipids macrocomponents such as myristic acid and vegetable oil do not decrease the dynamic adsorption capacity and recovery of the model PAH on SiO2-Ant. It was demonstrated that π-π stacking interaction with the analyte determine the selectivity of SiO2-Ant towards of anthracene. This makes SiO2-Ant attractive for selective pre-concentration of PAHs from high lipid content objects, such as vegetable oils.
Carrier Protein-Free Chemo-Enzymatic Synthesis of Arylomycin A2 and Structural Characterization of the Cytochrome P450 AryC
Authors: Aldemir Hülya , Shu Shuangjie , Schaefers Francoise , Hong Hanna , Richarz René , Harteis Sabrina , Einsiedler Manuel , Milzarek Tobias M. , Schneider Sabine , Gulder Tobias A. M.
Published: February 2022

The functional and structural evaluation of AryC, the cytochrome P450 performing biaryl coupling in biosynthetic arylomycin assembly, and its application in the chemo-enzymatic synthesis of arylomycin A2 is described. AryC efficiently converts free substrates without the requirement of any protein interaction partner, likely enabled by a strongly hydrophobic cavity at the surface of AryC pointing to the substrate tunnel. The resulting reactivity of AryC is unprecedented in cytochrome P450-mediated biaryl construction in non-ribosomal peptides, in which PCP-tethering so far was crucial both in vivo and in vitro. Our work thus provides a basis for the development of general biocatalytic platforms for the efficient biocatalytic synthesis of biaryl peptide antibiotics.
Intermolecular 2+2 Imine-Olefin Photocycloadditions Enabled by Cu(I)-Alkene MLCT
Authors: Flores Daniel , Neville Michael , Schmidt Valerie
Published: February 2022

2+2 Photocycloadditions are idealized, convergent approaches to the construction of 4-membered heterocyclic rings, including azetidines. However, methods of direct excitation are limited by the unfavorable photophysical properties of imines and electronically unbiased alkenes. Here, we report copper-catalyzed photocycloadditions of non-conjugated imines and alkenes to produce a variety of substituted azetidines. Ligand design allows this base metal-catalyzed method to achieve 2+2 imine-olefin photocycloaddition via selective alkene activation through a coordination-MLCT pathway.
Use of Marine biotoxins to modulate the tyrosine kinase domain of the human epidermal growth factor receptor
Authors: Arulanandam Charli Deepak , Dharmara Ramesh , Ragothaman Prathiviraj , Vincent Samuel Gnana Prakash
Published: February 2022

Inappropriate activation of the Epidermal growth factor receptor (EGFR) group of kinases has been identified in a variety of tumour cells, either due to mutation or overexpression. Although the tumour is a fatal disease, significant therapy discoveries have lately been made. The human EGFR and this family of kinases have emerged as promising targets for cancer therapy. In this molecular docking study, Natural marine toxins are employed to regulate the activity of the human EGFR tyrosine kinase domain (EGFRtkd) in the molecular docking investigation (PDB ID5JEB). Marine biotoxins can cause neurological, gastrointestinal, and cardiovascular problems, as well as severe mortality and long-term morbidity in some situations. Because there is no antidote for any of the natural marine poisons, supportive care is the mainstay of treatment. Paralytic shellfish poisoning, in particular, and puffer fish poisoning, in particular, can result in death within hours of exposure to the poisons and may require immediate medical intervention. However, this research found that marine biotoxins can modulate EGFRtkd. Furthermore, homoyessotoxin was anticipated to be an EGFRtkd modulator with a binding affinity as -9.584 kcal/mol. To employ the homoyessotoxin in tumour therapies, further knowledge of natural marine biotoxins and further toxicological research is required.
Structure determination of small molecule compounds by an electron diffractometer for 3D ED/MicroED
Authors: Ito Sho , White Fraser , Okunishi Eiji , Aoyama Yoshitaka , Yamano Akihito , Sato Hiroyasu , Ferrara Joseph , Jasnowski Michał , Meyer Mathias
Published: February 2022

3D electron diffraction (3D ED)/Micro electron diffraction (MicroED) has extended the limits of crystallography by enabling the determination of three dimensional molecular structures from sub-μm microcrystals. However, 3D ED/microED measurements using current state-of-the-art electron microscopes require experts in both electron microscopy and crystallography making the method rather difficult for researchers who simply need structures. Here, we present a diffractometer specifically designed for 3D ED/microED and show how it works for determining crystal structures. The newly developed electron diffractometer will provide many researchers with an easy path to structure determination of crystals that are less than 1 μm in size.
Acetate Facilitated Nickel Catalyzed Coupling of Aryl Chlorides and Alkyl Thiols
Authors: Oechsner Regina M. , Wagner J. Philipp , Fleischer Ivana
Published: February 2022

We report a mild, fast and convenient catalytic system for the coupling of aryl chlorides with primary, secondary, as well as previously challenging tertiary alkyl thiols using an air-stable nickel(II) precatayst in combination with the low-cost base potassium acetate at room temperature. This new catalytic system tolerates a variety of functional groups and enables the generation of thioethers for a wide range of substrates, including pharmaceutical compounds in excellent yields. Chemoselec-tive functionalization of disubstituted substrates was demonstrated. Kinetic and NMR-studies, as well as DFT computations support a Ni(0)/Ni(II) catalytic cycle and identify the oxidative addition product as the resting state. Acetate coordination and subsequent acetate facilitated formation of a thiolate complex via internal deprotonation play a key role in the catalytic cycle.
Azetidinium lead halide Ruddlesden-Popper phases
Authors: Tian Jiyu , Zysman-Colman Eli , Morrison Finlay
Published: February 2022

A family of Ruddlesden-Popper (n = 1) layered perovskite-related phases, Az2PbClxBr4-x with composition 0 ≤ x ≤ 4 were obtained using mechanosynthesis. A linear variation in unit cell volume as a function of anion average radius is observed. A tunable bandgap is achieved, ranging from 2.81 to 3.43 eV, and the bandgap varies in a second order polynomial relationship with the halide composition.
Inactivation of novel coronavirus and alpha variant by photo-renewable CuxO/TiO2 nanocomposites
Authors: Tatsuma Tetsu , Nakakido Makoto , Ichinohe Takeshi , Kuroiwa Yoshinori , Tomioka Kengo , Liu Chang , Miyamae Nobuhiro , Onuki Tatsuya , Tsumoto Kouhei , Hashimoto Kazuhito , Wakihara Toru
Published: February 2022

In order to reduce infection risk of novel coronavirus (SARS-CoV-2), we developed photocatalysts with nanoscale rutile TiO2 (4–8 nm) and CuxO (1–2 nm or less). Their extraordinarily small size leads to high dispersity and good optical transparency, besides large active surface area. Those photocatalysts can be applied to white and translucent latex paints and a transparent varnish. Although Cu2O clusters involved in the paint coating undergo gradual aerobic oxidation in the dark, the oxidized clusters are re-reduced under >380 nm light. The paint coating inactivated novel coronavirus and its alpha (B.1.1.7) variant under irradiation with fluorescent light for 3 h. The coating also exhibited antivirus effects on influenza A virus, feline calicivirus and bacteriophage Qβ. The photocatalysts would be applied to practical coatings and lower the risk of coronavirus infection via solid surfaces.
Empirical optimization of molecular simulation force fields by Bayesian inference
Authors: Köfinger Jürgen , Hummer Gerhard
Published: February 2022

The demands on the accuracy of force fields for classical molecular dynamics simulations are steadily growing as larger and more complex systems are studied over longer times. One way to meet these growing demands is to hand over the learning of force fields and their parameters to machines in a systematic (semi-)automatic man- ner. Doing so, we can take full advantage of exascale computing, the increasing availability of experimental data, and advances in quantum-mechanial computations and the calculation of experimental observables from molecular ensembles. Here, we discuss and illustrate the challenges we face in this endeavor and explore a way forward by adapting the Bayesian inference of ensembles (BioEn) method [Hummer and K ̈ofinger, J. Chem. Phys. (2015)] for force field parameterization. In the Bayesian inference of force fields (BioFF) method developed here, the optimization problem is regularized by a simplified prior on the force field parameters and an entropic prior act- ing on the ensemble. The latter compensates for the unavoidable over-simplifications in the parameter prior. We determine optimal force field parameters using an iterative predictor-corrector approach, in which we run simula- tions, determine the reference ensemble using the weighted histogram analysis method (WHAM), and optimize the BioFF posterior. We illustrate this approach for a simple polymer model, using the distance between two labeled sites as the experimental observable. By systematically resolving force field issues, the BioFF corrections extend to observables not included in ensemble reweighting. We envision future force field optimization as a formalized, systematic, and (semi-)automatic machine learning effort that incorporates a wide range of data from experiment and high-level quantum chemical calculations and takes advantage of exascale computing resources.
Photoelectrochemical uranium extraction from uranium mine tailings seepage water
Authors: Ye Yin , Jin Jian , Liang Yanru , Qin Zemin , Tang Xin , Feng Yanyue , Lv Miao , Miao Shiyu , Li Cui , Chen Fan , Wang Yuheng
Published: February 2022

Extracting uranium (U) from mine tailings seepage water can compensate the depletion of conventional U resources. However, current photocatalytic methods have intrinsic obstacles, such as the recombination of charge carriers, and the deactivation of catalysts by extracted U. Here we show that, by applying a small bias potential on the photocatalyst to drive spatial charge-carriers separation, the photoelectrochemical (PEC) method enables much faster U extraction and exceptional stability. In synthetic U-bearing water, the PEC U extraction proceeds via single-step one-electron reduction. Hence stable U(V) is produced from aqueous media under ambient conditions for the first time, implying the potential to facilitate future studies on U(V) chemistry. In real seepage water, the PEC method achieves a capacity of 0.67 gU m-3∙h-1 without further optimization, which is 17 times faster than the photocatalytic method using identical photocatalyst. The PEC U extraction method is therefore of broad research interests.
Drug Repurposing for Coronavirus (COVID-19): In Silico Screening of Known Drugs Against the SARS-CoV-2 Spike Protein Bound to Angiotensin Converting Enzyme 2 (ACE2) (6M0J)
Authors: Kalamatianos Konstantinos
Published: February 2022

E4/18-07-2021

E3/03-03-2021

Molecular Dynamics Simulation has been added to E2/21-12-2020

E2/21-12-2020

In this study FDA approved HCV antiviral drugs and their structural analogues – several of them in clinical trials - were tested for their inhibitory properties towards the SARS-CoV-2 Spike protein bound to angiotensin converting enzyme 2 (ACE2) (6M0J) using a virtual screening approach and computational chemistry methods. The most stable structures and the corresponding binding affinities of thirteen such antiviral compounds were obtained. Frontier molecular orbital theory, global reactivity descriptors, molecular docking calculations and electrostatic potential (ESP) analysis were used to hypothesize the bioactivity of these drugs against 6M0J. It is found that increased affinity for the protein is shown by inhibitors with large compound volume, relatively higher electrophilicity index, aromatic rings and heteroatoms that participate in hydrogen bonding. Amongst the drugs tested, four compounds 10-13 showed excellent results – binding affinities -11.2 to -11.5 kcal.mol-1. These four top scoring compounds may act as lead compounds for further experimental validation, clinical trials and even for the development of more potent antiviral agents against the SARS-CoV-2.

E1/24-08-2020

In this study FDA approved antiviral drugs and lopinavir analogues in clinical trials were tested for their inhibitory properties towards the SARS-CoV-2 Spike protein bound to

angiotensin converting enzyme 2 (ACE2) (6M0J) using a virtual screening approach and computational chemistry methods. Amongst the drugs tested, four compounds, PubChem CID 492005, CID 486507, CID 3010249 and

lopinavir showed excellent results – binding interactions -9.0 to -9.3 kcal.mol-1. These four top scoring compounds may act as lead compounds for further experimental validation, clinical trials and even for the development of more potent antiviral agents against the SARS-CoV-2.
Biaryl bond formation through biocatalytic oxidative cross-coupling reactions
Authors: Zetzsche Lara , Yazarians Jessica , Chakrabarty Suman , Hinze Meagan , Lukowski April , Joyce Leo , Narayan Alison
Published: February 2022

Biocatalysis offers compelling advantages in synthesis, often becoming the method of choice based on sustainability, safety, and selectivity considerations. Despite these advantages, enzymes in synthesis are typically dedicated to functional group interconversions in linear synthetic sequences and have not been broadly integrated into the retrosynthetic logic for carbon skeleton assembly. In this article, we disclose a biocatalytic platform for fragment coupling to assemble target molecules convergently. Specifically, we report a strategy for biocatalytic phenolic cross-coupling through oxidative C–C bond formation. Using cytochrome P450 enzymes, we demonstrate the ability to catalyze cross-coupling reactions on a panel of phenolic substrates and further demonstrate the ability to tune these catalysts to possess the desired reactivity, site-, and atroposelectivity. This streamlined method for constructing sterically-hindered biaryl bonds provides an engineerable platform for assembling molecules with programmable catalyst-controlled reactivity and selectivity unprecedented with small molecule catalysts.