bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryoradiolysis of oxygenated cytochrome P450 17A1 with lyase substrates generates expected products
Authors: Usai Remigio , Denisov Ilia , Sligar Stephen , Kincaid James
Published: February 2022

When subjected to γ-irradiation at cryogenic temperatures the oxygenated complexes of Cytochrome P450 17A1 bound with either of the lyase substrates, 17-OH PREG or 17-OH PROG are shown here to generate the corresponding lyase products, dehydroepiandrosterone (DHEA) and androstenedione (AD) respectively. The current study uses gas chromatography-mass spectrometry (GC/MS) to document the presence of the initial substrates and products in extracts of the processed samples. A rapid and efficient method for the simultaneous determination of residual substrate and products by GC/MS is described without derivatization of the products. It is also shown that no lyase products were detected for similarly treated control samples containing no nanodisc associated CYP17 enzyme, demonstrating that the product is formed during the enzymatic reaction and not by GC/MS conditions nor the conditions produced by the cryoradiolysis process.
Tuning Coordination Modes and Nucleation of Calcium Phosphate with Oligomeric Lactic Acid and pH Values: Theoretical and Experimental Study
Authors: Chen Hongwei , Lv Changchang , Guo Lin , Ma Ming , 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

Mineralization of calcium phosphate (CaP) is ubiquitous in nature, which can facilitate biological organisms produce hierarchically structured minerals. The influences of the addition of oligomeric lactic acid (LACn, n=1, 8) and changing pH values on nucleation processes of CaP under the simulated body fluid (SBF) solution or aqueous solution were revealed by using ab initio molecular dynamics (AIMD) and molecular dynamics (MD) simulations. Through increasing pH value, the coordination between differently protonated phosphate species and Ca2+ ions could be tuned from the monodentate (η1) to the coexisting monodentate and bidentate (η2) modes. The carboxyl and hydroxyl groups of LAC molecules are capable of forming multiple interactions such as proton transfer, electrostatic interaction, and intermolecular hydrogen bonding with phosphate species and Ca2+ ions on both pre-nucleation clusters and hydroxyapatite (HA) surfaces. The high-throughput experimentations (HTE) with factors of the adding LAC, changing Ca/P ratios (1.25 ~ 2.50), using different solutions demonstrated that the UV-Vis absorbance values decreased with addition of LAC, indicating the inhibition of the nucleation process of CaP. At the physiological pH of 7.4, the CaP samples with different Ca/P ratios (1.50, 1.67 and 2.00) exhibited negative zeta potential values, which were correlated with the surface electrostatic potential distributions and potential biological applications. The precipitation was CaHPO4·2H2O (DCPD) in neutral condition at the early stage of nucleation process. Understanding the effects of different pH and Ca/P values on the nucleation process and interfacial interaction between LAC additive and the nanocluster is helpful to guide the rational design of biocompatible materials.
Reviving the Coordination Chemistry of Sulfonium Cations
Authors: Li Ruiping , Barel Nitsan , Subramaniyan Vasudevan , Cohen Orit , Tibika Francoise , Tulchinsky Yuri
Published: February 2022

ABSTRACT: More than a century old, sulfonium ions are still intriguing species in the landscape of organic chemistry. On one hand they have found broad applications in organic synthesis and material science, but on the other hand, while isoelectronic to the ubiquitous tertiary phosphine ligands, their own coordination chemistry has been neglected for the last three decades. Here we report the synthesis and full characterization of the first Rh(I) and Pt(II) complexes of sul-fonium. Moreover, for the first time, the coordinating ability of an aromatic sulfonium has been established. A thorough computational analysis of the exceptionally short S-Rh bonds obtained attests for the strongly π-accepting nature of sul-fonium cations and places them among the best π-acceptor ligands available today. Our calculations also show that when embedded within a pincer framework their π-acidity is enhanced. Therefore, in addition to the stability and modularity that these frameworks offer, our pincer complexes might open the way for sulfonium cations to become powerful tools in π-acid catalysis.
Controllable Antibacterial Activity through Acid-Triggered Molecular Cage Release of Stored Ag+
Authors: Zhu Wencheng , Yu Haitao , Luo Yanju , Chen Shunwei , Zheng Xujun
Published: February 2022

Aiming for solving the emergence of drug-resistant bacteria worldwide, the construction of novel supramolecular self-assembly systems with antibacterial functions is attracting growing research attention. Herein, using dynamically reversible Schiff-base imine bonds as the assembly strategy, a three-dimensional pure organic cage, namely 4-cage, was obtained in high yield. By taking advantage of the bidentate chelating capability of its imine-based skeleton, 4-cage was demonstrated to serve as an Ag+-carrier. Owing to the acid-induced decomposition of this skeleton, the Ag+-loaded 4-cage can controllably release Ag+ through pH regulation, hence, as a proof-of-concept, it is proved to be applicable as a controllable release antibacterial reagent. Such pH-responsive Ag+-carried supramolecular architecture may shed light on the molecule design strategies for bacterial elimination in different environments, or for controllable functions in various other fields.
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 exhibited favourable biocatalyst loading, light utilisation and electron flux output, ultimately almost doubling the photocurrent of state-of-the-art porous structures of the same height. When the micropillars’ heights were increased from 50 to 600 µm, milestone mediated photocurrent densities of 245 µA cm–2 (the closest thus far to theoretical predictions) and external quantum efficiencies of up to 29% could be reached. This study demonstrates how bioenergy from photosynthesis could be more efficiently harnessed in the future and provide new tools for 3D electrode design.
Impacts of Porous Silica-Nanoencapsulated Pesticide Applied to Soil on Plant Growth and Soil Microbial Community
Authors: Bueno Vinicius , Wang Peiying , Harrisson Orfeo , Bayen Stephane , Ghoshal Subhasis
Published: February 2022

Porous silica nanocarriers have the potential to improve agricultural crop productivity. However, the impacts of nanoencapsulated pesticides on soil health and plant growth, and how they compare with conventional pesticide have not been systematically elucidated. In this study, we investigated how applying azoxystrobin encapsulated in porous hollow SiO2 nanocarriers to agricultural soil impacted the soil microbial community and plant development, using Solanum lycopersicum grown in the laboratory in soil microcosms. The data show that plant growth was heavily inhibited by the non-encapsulated pesticide treatment compared to that with encapsulated pesticide yielding 3.85-fold less plant biomass, while the soil microbial community experienced few to no changes regardless of the treatment. There was a 2.7-fold higher azoxystrobin uptake per unit dry plant biomass after 10 days of exposure for the non-encapsulated pesticide treatment when compared to that of nanoencapsulated pesticide, but only 1.5-fold increase in total uptake. After 20 days of exposure, however, the total uptake and uptake per unit of dry biomass were 3-fold and 10-fold higher, respectively, for the nanopesticide treatment. The differences in uptake can be attributed to phytotoxicity caused by the high the bioavailability of the non-encapsulated pesticide. The nanocarrier promoted slow release of the pesticide over days, which prevented phytotoxicity, and allowed healthy plant growth.
Machine Learning-Guided Discovery of 19F MRI Agents Enabled by Automated Copolymer Synthesis
Authors: Reis Marcus , Gusev Filipp , Taylor Nicolas , Chung Sang Hun , Verber Matthew , Lee Yueh , Isayev Olexandr , Leibfarth Frank
Published: February 2022

Modern polymer science is plagued by the curse of multidimensionality; the large chemical space imposed by including combinations of monomers into a statistical copolymer overwhelms polymer synthesis and characterization technology and limits the ability to systematically study structure–property relationships. To tackle this challenge in the context of 19F MRI agents, we pursued a computer-guided materials discovery approach that combines synergistic innovations in automated flow synthesis and machine learning (ML) method development. A software controlled, continuous polymer synthesis platform was developed to enable iterative experimental–computational cycles that resulted in the synthesis of 397 unique copolymer compositions within a six-variable compositional space. The non-intuitive design criteria identified by ML, which was accomplished by exploring less than 0.9% of overall compositional space, upended conventional wisdom in the design of 19F MRI agents and lead to the identification of >10 copolymer compositions that outperformed state-of-the-art materials.
Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design
Authors: Khalak Yuriy , Tresadern Gary , Aldeghi Matteo , Baumann Hannah Magdalena , Mobley David L. , de Groot Bert L. , Gapsys Vytautas
Published: February 2022

The recent advances in relative protein-ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains a challenging endeavour, mostly limited to small model cases. Here, we demonstrate accurate first principles based absolute binding free energy estimates for 128 pharmaceutically relevant targets. We use a novel rigorous method to generate protein-ligand ensembles for the ligand in its decoupled state. Not only do the calculations deliver accurate protein-ligand binding affinity estimates, but they also provide detailed physical insight into the structural determinants of binding. We identify subtle rotamer rearrangements between apo and holo states of a protein that are crucial for binding. When compared to relative binding free energy calculations, obtaining absolute binding free energies is considerably more challenging in large part due to the need to explicitly account for the protein in its apo state. In this work we present several approaches to obtain apo state ensembles for accurate absolute ΔG calculations, thus outlining protocols for prospective application of the methods for drug discovery.
Spin states, bonding and magnetism in mixed valence iron(0)–iron(II) complexes
Authors: Kim Daniel , Wilson Daniel , Fataftah Majed , Mercado Brandon , Holland Patrick
Published: February 2022

We report the synthesis of two complexes featuring unsupported Fe–Fe bonds between a diketiminate/dialdiminate-coordinated iron site and a cyclopentadienyl dicarbonyl iron site. Mössbauer spectroscopy, SQUID magnetometry and computational analysis indicate that the most accurate electronic structure description is with the Fe(CO)2Cp site as low spin iron(0), and it acts as a Lewis base toward the high spin iron(II) of the LFe fragment which is a Lewis acid. In both compounds, the three-coordinate high-spin iron(II) site has large zero-field splitting (zfs), up to D = –50 cm–1.
Finite Element Modeling of the Dielectric Response of Metal/Metal Oxide Nanocomposites: Coarse-Graining the Quantum Response
Authors: Henderson Brett , Adluri Archita , Paci Irina
Published: February 2022

Nanocomposite materials with metallic or ceramic inclusions show great promise as highly-tunable functional materials, particularly for applications where high dielectric permittivities are desirable, such as charge-storage or energy-storage materials. These applications present a challenge for computational approaches, as the field response of the nanoscale inclusion is quantum in nature, yet any representative sample of the material must encompass hundreds if not thousands of atoms. As currently implemented, finite element methods offer some predictive power for macroscale matrix-inclusion composites. However, their applicability cannot necessarily be extended to few-nanometer, molecular scale inclusions, where quantum and interfacial effects gain importance in the overall response to the applied field. Here, we develop an adjustable finite element method approach to calculate the low frequency dielectric constant of composites consisting of a metal-oxide matrix with molecular-scale silver inclusions, by introducing an interfacial layer in the general model. A process for coarse-graining atomistic ab initio results to generate best fit finite element models is also laid out in this work. We show that a continuum model informed by ab initio results can capture many of the relevant polarization effects in a metal/metal oxide nanocomposite, at a fraction of the computational cost.
The potential scarcity, or not, of polymeric overall water splitting photocatalysts
Authors: Saunders Benedict , Wilbraham Liam , Prentice Andrew , Sprick Reiner Sebastian , Zwijnenburg Martinus Antonius
Published: February 2022

We perform a high-throughput computational screening of a set of 3240 conjugated alternating binary co-polymers and homo-polymers, in which we predict their ability to drive sacrificial hydrogen evolution and overall water splitting when illuminated with visible light. We use the outcome of this screening to analyse how common the ability to drive either reaction is for conjugated polymers loaded with suitable co-catalysts, and to suggest promising (co-)monomers for polymeric overall water splitting catalysts.
Singlet and triplet excited-state dynamics of a nonfullerene electron acceptor Y6
Authors: Natsuda Shin-ichiro , Sakamoto Yuji , Takeyama Taiki , Shirouchi Rei , Saito Toshiharu , Tamai Yasunari , Ohkita Hideo
Published: February 2022

Understanding the excited-state dynamics of nonfullerene electron acceptors is essential for further improvement of organic solar cells. Herein, we investigated the singlet and triplet excited-state dynamics in Y6, a novel nonfullerene acceptor, using transient absorption spectroscopy. We found that pristine Y6 films show biphasic singlet exciton decay kinetics with decay constants of ~220 ps and ~1200 ps, which is the origin of the large discrepancies in the previously reported exciton lifetimes in the solid state. The majority of the Y6 singlet excitons decayed with the faster (~220 ps) component, whereas a clear photoluminescence with the slower (~1200 ps) component was observed. Y6 singlet excitons undergo fast diffusion in the crystalline domains, resulting in fast singlet–singlet exciton annihilation, after which ultrafast triplet formation, assigned to singlet fission from higher excited singlet states, is observed.
Real-space Imaging of the Multiple Halogen Bonds by Ultrahigh-resolution Scanning Probe Microscopy
Authors: Wang Dingguan , Wang Zishen , Liu Wei , Arramel Arramel , Zhong Siying , Wee Andrew
Published: February 2022

Understanding the physical origin of STM/AFM image contrast is of significance for not only promoting surface characterization techniques, but also probing surface nanostructures with the atomic/sub-molecular resolution. Herein, we demonstrate the real-space imaging of halogen bonds acquired by non-contact atomic force microscopy (nc-AFM)/bond-resolution scanning tunneling microscopy (BR-STM) with functional CO-tip, and study the image contrast origin of halogen bonds. The presence of bright line features is associated to the specific site where halogen bond forms, which is experimentally evidenced to be contributed by both CO-tip bending and electron density exchange. Three distinct types of halogen bonds are observed, which origin from the noncovalent interactions of Br-atoms with positive potential H-atom, neutral potential Br-atom and negative potential N-atom, respectively. Our work shows that nc-AFM and BR-STM can directly image halogen bonds and can be used to unambiguously discriminate their bonding features. This work demonstrates the potential use of this technique to image other non-covalent intermolecular bonds and to understand complex supramolecular assemblies at the sub-molecular level.
Environment-dependent Emission Tuning in the Multicolor Nitrogen-doped Carbon Quantum Dots
Authors: Sengottuvelu Dineshkumar , Shaik Abdul Kalam , Mishra Satish , Abbaszadeh Mahsa , Hammer Nathan , Kundu Santanu
Published: February 2022

Carbon quantum dots (CQDs) are fascinating luminous materials from the carbonaceous family and are increasingly being investigated in many optoelectronic applications due to their unique photoluminescence (PL) characteristics. Herein, we report the synthesis of nitrogen-doped carbon quantum dots (NCQDs) from citric acid and m-phenylenediamine using a one-pot hydrothermal approach. The environment-dependent emission changes of NCQDs were extensively investigated in various solvents, in solid-state, and in physically assembled PMMA-PnBA-PMMA copolymer gels in 2-ethyl hexanol. The NCQDs display bright emission in various solvents as well as in solid-state and a temperature-dependent enhanced emission in gels. In detail, these NCQDs exhibit multicolor PL emission across the visible region and its enhancement upon changing the environment (solutions and polymer matrices). The NCQDs also exhibit excitation-dependent PL and solvatochromism, which are rarely observed in CQDs. Most CQDs are non-emissive in the aggregated or solid-state due to the aggregation-caused quenching (ACQ) effect, limiting their solid-state applications. However, these NCQDs display a strong solid-state emission centered at 568 nm ascribed to the presence of abundant surface functional groups, which helps to prevent the - interaction between the NCQDs and to overcome the ACQ effect in the solid-state. Interestingly, the NCQD containing gels display a significant fluorescence enhancement than the NCQDs in 2-ethyl hexanol solution because of the interaction between the polar PMMA blocks and NCQDs. This research opens up the development of large-scale, low-cost multicolor phosphor for the fabrication of optoelectronic devices, sensing, and bioimaging applications.
Direct measurement of oxygen mass transport at the nanoscale
Authors: Baiutti Federico , Chiabrera Francesco , Diercks David , Cavallaro Andrea , Yedra Lluis , Lopez-Conesa Lluis , Morata Alex , Estradé Sonia , Peiró Francesca , Aguadero Ainara , Tarancon Albert
Published: February 2022

Tuning oxygen mass transport properties at the nanoscale offers a promising approach for developing high performing energy materials. A number of strategies for engineering interfaces with enhanced oxygen diffusivity and surface exchange has recently been proposed. However, the origin and the local magnitude of such local effects remain largely undisclosed to date. This is ascribed to the lack of direct measurement tools with sufficient resolution. In this work, we use atom probe tomography with sub-nanometric resolution to study oxygen mass transport on oxygen-isotope exchanged thin films of lanthanum chromite. We present a direct visualization of nanoscaled highly conducting oxygen incorporation pathways along grain boundaries, with reliable quantification of fast oxygen diffusion at grain boundaries and correlative link to local chemistries. Combined with finite element simulations of the precise 3D nanostructure, we quantify an enhancement in the grain boundary oxygen diffusivity and in the surface exchange coefficient of lanthanum chromite of about 4 and 3 orders of magnitude, respectively, compared to the bulk. This remarkable increase of the oxygen diffusivity in an interface-dominated material is unambiguously attributed to grain boundary conduction highways thanks to the use of a powerful technique that can be straightforwardly extended to the study of currently inaccessible multiple nanoscale mass transport phenomena.
Thickness of graphene oxide-based materials as a control parameter
Authors: ESTEBAN ARRANZ ADRIÁN , Arranz Miguel Ángel , Morales Mónica , Martin-Folgar Raquel , Álvarez-Rodríguez Jesús
Published: February 2022

Graphene oxide-based materials have been widely used for different applications, such as: biotechnology, electronics, and adsorption or separation technologies amongst other uses. In this study, graphite oxide (GrO), large graphene oxide (lGO) and small graphene oxide (sGO) were synthesized. Monolayer large graphene oxide (mlGO) was detected and isolated in this synthesis prior to lGO separation from GrO. A battery of techniques was applied to elucidate their physicochemical properties. Morphological results acquired by high resolution scanning electron microscopy, transmission electron microscopy and scanning transmission electron microscopy demonstrated the flat and planar structures of these materials. Similar lateral dimensions were found for lGO and mlGO unlike sGO. However, based on atomic force microscopy studies, it was able to demonstrate that lGO presented thicker laminar structures than mlGO. Their crystallography evaluated by x-ray diffraction corroborated the results obtained by the atomic force microscopy studies, since mlGO displayed a diffractogram characteristic of highly exfoliated material. Additionally, Turbiscan experiments revealed a more significant impact from the thickness of these materials in contrast to their lateral dimensions in their colloidal stability properties in aqueous solution. Characterization results were correlated with the optical band gap obtained from the Tauc method of their UV-vis absorption spectra, which could be implemented to characterize in-line the production of these carbon materials to optoelectronic devices.
Experimental and DFT Studies on Cp*Co(III)-Catalyzed Selective C8-Olefination and Oxyarylation of Quinoline N-Oxides with Terminal Alkynes
Authors: Sharma Upendra , Parmar Diksha , Dhiman Ankit Kumar , Kumar Rohit , Sharma Akhhilesh K
Published: February 2022

Herein we report Cp*Co(III)-catalysed site-selective (C8)-H olefination and oxyarylation of quinoline N-oxides with terminal alkynes. The selectivity for C8-olefination and oxyarylation is sterically and electronically controlled. In case of quinoline N-oxides (unsubstituted at C2-position), only olefination product is obtained irrespective of the nature of alkynes. In contrast, majorly oxyarylation is observed when 2-substituted quinoline N-oxides are reacted with bulkier alkynes such as 9-ethynyl phenanthrene. However, alkynes with electron-withdrawing groups provided only olefination products with 2-substituted quinoline N-oxides also. The developed strategy allowed a facile functionalization of naturally derived quinoline N-oxides and terminal alkynes to deliver corresponding olefinated and oxyarylated products. In the developed protocol, the 'N-O’ bond played a dual role i.e., as a traceless directing group and an oxygen atom source (in case of oxyarylation), which is confirmed by 18O-labeling and crossover experiments. In addition, control experiments, deuterium labeling experiments, KIE studies and DFT studies are performed to understand the mechanism and origin of selectivity for different substrates. DFT studies revealed that the alkyne addition into Co-C bond is the rate limiting step. The observed product selectivity is reproduced by DFT methods. Furthermore, the energy decomposition analysis is performed to understand the origin of selec-tivity.
Exploring the Solution Formation of UiO Family Hf Metal-Organic Framework clusters with in situ X-Ray Pair Distribution Function Analysis
Authors: Firth Francesca C.N. , Gaultois Michael W. , Wu Yue , Stratford Joshua , Keeble Dean S. , Grey Clare P. , Cliffe Matthew J.
Published: February 2022

The structures of Zr and Hf metal-organic frameworks (MOFs) are very sensitive to small changes in synthetic conditions. One key difference affecting the structure of UiO MOF phases is the shape and nuclearity of Zr or Hf metal clusters acting as nodes in the framework; although these clusters are crucial, their evolution during MOF synthesis is not fully understood. In this paper, we explore the nature of Hf metal clusters which form in different reaction solutions, including in a mixture of DMF, formic acid and water. We show that the choice of solvent and reaction temperature in UiO MOF syntheses determines the cluster identity and hence the MOF structure. Using in situ X-ray pair distribution function measurements, we demonstrate that the evolution of different Hf cluster species can be tracked during UiO MOF synthesis, from solution stages to the full crystalline framework, and use our understanding to propose a formation mechanism for the hcp UiO-66(Hf) MOF, in which first the metal clusters aggregate from the M6 cluster (as in fcu UiO-66) to the hcp-characteristic M12 double cluster, and following this, the crystalline hcp framework forms. These insights pave the way towards rationally designing syntheses of as-yet unknown MOF structures, via tuning the synthesis conditions to select different cluster species.
Catalytic synthesis of 1H-2-benzoxocins; Cobalt(III)-carbene radical approach to 8-membered heterocyclic enol ethers
Authors: Zhou Minghui , Wolzak Lukas A. , Li Zirui , de Zwart Felix J. , Mathew Simon , de Bruin Bas
Published: February 2022

The metallo-radical activation of ortho-allylcarbonyl-aryl N-arylsulfonylhydrazones with the paramagnetic cobalt(II) porphyrin catalyst [Co^II(TPP)] (TPP = tetraphenylporphyrin) provides an efficient and powerful method for the synthesis of novel 8-membered heterocyclic enol ethers. The synthetic protocol is versatile, practical and enables the synthesis of a wide range of unique 1H-2-benzoxocins in high yields. The catalytic cyclization reactions proceed with excellent chemoselectivities, have a high functional group tolerance, and provide several opportunities for the synthesis of new bioactive compounds. The reactions are shown to proceed via cobalt(III)-carbene radical intermediates, which are in-volved in intramolecular hydrogen transfer (HAT) from the allylic position to the carbene radical, followed by a near barrierless radical rebound step in the coordination sphere of cobalt. The proposed mechanism is supported by experi-mental observations, density functional theory (DFT) calculations and spin trapping experiments.
Dimsyl Anion Enables Visible-Light-Promoted Charge Transfer in Cross-Coupling Reactions of Aryl Halides
Authors: Pan Lei , Cooke Maria Victoria , Spencer Amara , Laulhé Sébastien
Published: February 2022

A simple and mild methodology is reported for visible-light-promoted synthesis of unsymmetrical chalconides ena- bled by dimsyl anion in the absence of transition-metals or photoredox catalysts. The cross-coupling reaction between aryl halides and diaryl dichalconides proceeds in good to excellent yields with electron-rich, electron-poor, and heteroaromatic moieties. Mechanistic investigations using UV−Vis spectroscopy, time-dependent density functional theory (DFT) calculations, and control reactions suggest that dimsyl anion forms an electron-donor-acceptor (EDA) complex capable of absorbing blue light, leading to a charge transfer responsible for generation of aryl radicals from aryl halides. This previously unreported mechanistic pathway may be applied to other light-induced transformations performed in DMSO in the presence of bases and aryl halides.
Radical–Anion Coupling Through Reagent Design: Hydroxylation of Aryl Halides
Authors: Greener Andrew J. , Ubysz Patrycja , Owens-Ward Will , Smith George , Whitwood Adrian C. , James Michael J.
Published: February 2022

The design and development of an oxime-based hydroxylation reagent, which can chemoselectively convert aryl halides (X = F, Cl, Br, I) into phenols under operationally simple, transition-metal-free conditions is described. Key to the success of this approach was the identification of a reducing oxime anion which can interact and couple with open-shell aryl radicals. Experimental and computational studies support the proposed radical-nucleophilic substitution chain mechanism.
Surface properties modulate protein corona formation and determine cellular uptake and cytotoxicity of silver nanoparticles
Authors: Barbalinardo Marianna , Bertacchini Jessika , Bergamini Linda , Magarò Maria Sara , Ortolani Luca , Sanson Alessandra , Palumbo Carla , Cavallini Massimiliano , Gentili Denis
Published: February 2022

The lack of the basic understanding of how NPs interact with the biological environment has severely limited their delivery efficiency to target tissue and clinical translation. Here, we show the effective regulation of the surface properties of NPs, cellular uptake and cytotoxicity. Surface properties of NPs are tuned through the controlled replacement of native ligands, which favor protein adsorption, with ligands able to increase protein adsorption resistance. The extent and composition of the protein layer adsorbed on NPs are strongly correlated to the degree of ligands replaced on their surface and, while BSA is the most abundant protein detected, ApoE is the one whose amount is most affected by surface properties. Increasing the protein resistance, cellular uptake and cytotoxicity in mouse embryonic fibroblasts of NPs are drastically reduced, but surface coating has not effects on the process by which NPs mainly induce cell death.
Determining the Self-Limiting Electrospray Deposition Compositional Limits for Mechanically Tunable Polymer Composites
Authors: Green-Warren Robert , Bontoux Luc , McAllister Noah , Kovacevich Dylan , Shaikh Asaad , Kuznetsova Christianna , Tenorio Max , Lei Lin , Pelegri Assimina , Singer Jonathan
Published: February 2022

Electrospray deposition (ESD) is a versatile micro/nano coating technology that utilizes the competition between surface charge of a droplet and its surface tension to create monodisperse generations of micro/nano droplets. ESD can deposit uniform thin films by including dilute solutes in these droplets. One mode of ESD, self-limiting electrospray deposition (SLED), has been shown to exist when glassy polymers are sprayed in a volatile solvent below the polymer glass transition temperature (Tg). This leads to charge accumulation on the coating surface that slows the growth of the film thickness. Since solutes can be easily blended in dilute ESD solutions, we investigate the SLED limits of self-limiting and non-self-limiting solute blends. As a motivating application, we focus on mechanical properties of the film. Specifically, we blend self-limiting polystyrene (PS) and SU-8 epoxy resin with different non-self-limiting mechanical modifiers, such as plasticizers and curing agents. To characterize the resulting morphologies and mechanical properties, we employ scanning electron microscopy and nanoindentation of as received and smoothed films. The results illustrate the formation of composited polymers that exhibit self-limiting ability by SLED, depending on the interaction between the two components. Further, mechanical properties could be effectively fine-tuned within these compositional ranges. This signifies the 3D coating capabilities through SLED can be implemented incorporating additional functionalities and properties beyond the base matrix.
Structure determination of small molecule compounds by an electron diffractometer Synergy-ED
Authors: Ito Sho , White Fraser , Okunishi Eiji , Aoyama Yoshitaka , Yamano Akihito , Sato Hiroyasu , Ferrara Joseph , Jasnowski Michał , Meyer Mathias
Published: February 2022

Micro Electron Diffraction (MicroED) has extended the limits of crystallography by enabling the determination of three dimensional molecular structures from sub-μm microcrystals. However, 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 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.
Topology-Mediated Enhanced Polaron Coherence in Covalent Organic Frameworks
Authors: Ghosh Raja , Paesani Francesco
Published: February 2022

We employ the Holstein model for polarons to investigate the relationship among defects, topology, Coulomb trapping, and polaron delocalization in covalent organic frameworks (COFs). We find that intra-sheet topological connectivity and pi-column density can override disorder-induced deep traps and significantly enhance polaron migration by several orders of magnitude in good agreement with recent experimental observations. The combination of percolation networks and micropores makes trigonal COFs ideally suited for charge transport followed by kagome/tetragonal, and hexagonal structures. By comparing the polaron spectral signatures and coherence numbers of large 3D frameworks having a maximum of 180 coupled chromophores, we show that controlling nanoscale defects and the location of the counter anion is critical for the design of new COF-based materials yielding higher mobilities. Our analysis establishes design strategies for enhanced conductivity in COFs which can be readily generalized to other classes of conductive materials such as metal-organic frameworks and perovskites.
Absorption and scattering in perfect thermal radiation absorber-emitter metasurfaces
Authors: Nishijima Yoshiaki , To Naoki , Balcytis Armandas , Juodkazis Sauliur
Published: February 2022

Detailed spectral analysis of radiation absorption and scattering behaviors of metasurfaces was carried out via finite-difference time-domain (FDTD) photonic simulations. It revealed that, for typical metal-insulator-metal (MIM) nanodisc metasurfaces, absorbance and scattering cross-sections exhibit a ratio of Sabs/Ssca = 1 at the absorption peak spectral position. This relationship was likewise found to limit the attainable photo-thermal conversion efficiency in experimental and application contexts. By increasing the absorption due to optical materials, such as Cr metal nano-films typically used as an adhesion layer, it is possible to control the total absorption efficiency h = Sabs/Ssca and to to make it the dominant extinction mechanism. This guided the design of MIM metasurfaces tailored for near-perfect-absorption and emission of thermal radiation. We present the fabrication as well as the numerical and experimental spectral characterization of such optical surfaces.
Highly optically responsive divalent benzimidazolium-based axles as self-reporting pseudorotaxanes
Authors: Taimoory S. Maryamdokht , Yu Xiao , Beyeh N. Kodiah , Trant John F.
Published: February 2022

Mono and (bis)benzimidazoliums were evaluated both experimentally and computationally for their potential as building blocks of pseudopolyrotaxane axles. Their aggregation and optical behavior, along with their potential to form a [2]pseudorotaxane with dibenzyl-24-crown-8, was studied through the synergistic application of 1D/2D and diffusion ordered NMR spectroscopy, mass spectrometry, ultraviolet-visible & fluorescence spectroscopy, and time-dependent density functional theory. Their unique optical behaviour was measured and modeled as a function of protonation state, solvent, and concentration. The axles show strong solvochromaticism and a very pronounced concentration-dependent optical profile, including self-quenching when a pseudorotaxane is formed. This axle with multiple recognition sites, has the potential to form pseudorotaxanes with tunable optical behavior
Single–Ion Conducting Polymer Nanoparticles as Functional Fillers for Solid Electrolytes in Lithium Metal Batteries
Authors: Porcarelli Luca , Sutton Preston , Bocharova Vera , Aguirresarobe Robert , Zhu Haijin , Goujon Nicolas , Leiza Jose , Sokolov Alexei , Forsyth Maria , Mecerreyes David
Published: February 2022

Composite solid electrolytes including inorganic nanoparticles or nanofibers which improve the performance of polymer electrolytes due to their superior mechanical, ionic conductivity or lithium transference number are actively being searched for applications in lithium metal batteries. However, inorganic nanoparticles present limitations such as its tedious surface functionalization and agglomeration issues and poor homogeneity at high concentrations in polymer matrices. In this work, we report on polymer nanoparticles with lithium sulfonamide surface functionality (LiPNP) for application as electrolytes in lithium metal battery. The particles are prepared by semibatch emulsion polymerization, an easily up–scalable technique. LiPNPs are used to prepare two different families of particle reinforced solid electrolytes. When mixed with polyethylene oxide and lithium bis(trifluoromethane)sulfonimide (LiTFSI/PEO), the particles provoke a significant stiffening effect (E´ > 106 Pa vs. 105 Pa at 80 ºC) while retaining high ionic conductivity (σ = 6.6 × 10–4 S cm–1). Preliminary testing in LiFePO4 full cells, showed promising performance of the PEO nanocomposite electrolytes. By mixing the particles with propylene carbonate without any additional salt, we obtain true single ion conducting gel electrolytes as the lithium sulfonamide surface functionalities are the only sources of lithium ions in the system. The gel electrolytes are mechanically robust (up to G´ =106 Pa) and show ionic conductivity up to 10–4 S cm–1. Finally, the PC nanocomposite electrolytes were tested in symmetrical lithium cells. Our findings suggest that all–polymer nanoparticles could represent a new building block material for solid–state lithium metal battery applications.
Systematic QM Region Construction in QM/MM Calculations Based on Uncertainty Quantification
Authors: Brandt Felix , Jacob Christoph
Published: February 2022

While QM/MM studies of enzymatic reactions are widely used in computational chemistry, the results of such studies are subject to numerous sources of uncertainty, and the effect of different choices by the simulation scientist that are required when setting up QM/MM calculations is often unclear. In particular, the selection of the QM region is crucial for obtaining accurate and reliable results. Simply including amino acids by their distance to the active site is mostly not sufficient as necessary residues are missing or unimportant residues are included without evidence. Here, we take a first step towards quantifying uncertainties in QM/MM calculations by assessing the sensitivity of QM/MM reaction energies with respect to variations of the MM point charges. We show that such a point charge variation analysis (PCVA) can be employed to judge the accuracy of QM/MM reaction energies obtained with a selected QM region, and devise a protocol to systematically construct QM regions that minimize this uncertainty. We apply such a PCVA to the example of catechol \textit{O}-methyltransferase, and demonstrate that it provides a simple and reliable approach for the construction of the QM region. Our PCVA-based scheme is computationally efficient and requires only calculations for a system with a minimal QM region. Our work highlights the promise of applying methods of uncertainty quantification in computational chemistry.
Will the Chemical Probes Please Stand Up?
Authors: Škuta Ctibor , Southan Christopher , Bartunek Petr
Published: February 2022

This work provides a uniquely comprehensive and comparative overview of chemical probe sources and targets. This will be maintained and expanded for experts and non-informaticions seeking chemical probes to use in their work. We have analysed 940 experimental and 3,670 calculated probe candidates. Together these have evidence of specific binding for 796 human proteins across the target classes. We have flagged unsuitable (i.e. potentially misleading and resource-wasting) compounds from both probe groups. Compared to ChEMBL approved drugs, probes tend to be larger and more complex structures.
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 manner. 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 Köfinger, 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 acting 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.
Dual-functional cobalt catalyst enables electrocatalytic allylic C–H alkylation
Authors: Chen Ming , Wu Zheng-Jian , Song Jinshuai , Xu Hai-Chao
Published: February 2022

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

Previously, the ubiquitous issue regarding severe wasting of computational resources in all forms of molecular simulations due to repetitive local sampling was raised, and the local free energy landscape approach was proposed to address it. This approach is derived from a simple idea of first learning local distributions, and followed by dynamic assembly of which to infer global joint distribution of a target molecular system. When compared with conventional explicit solvent molecular dynamics simulations, a simple and approximate implementation of this theory in protein structural refinement harvested acceleration of about six orders of magnitude without loss of accuracy. While this initial test revealed tremendous benefits for addressing repetitive local sampling, there are some implicit assumptions need to be articulated. Here, I present a more thorough discussion of repetitive local sampling; potential options for learning local distributions; a more general formulation with potential extension to simulation of near equilibrium molecular systems; generalization of repetitive local sampling to repetitive local computation and potential application in accelerating numerical solving of complex equations; the prospect of developing computation driven molecular science; and the connection to mainstream residue pair distance distribution based protein structure prediction/refinement. This more general development is termed the local distribution theory to release the limitation of strict thermodynamic equilibrium in its potential wide application in both soft condensed molecular systems and complex equations.
A Computational Protocol to Calculate the Phosphorescence Energy of Pt (II) Complexes: Is the lowest triplet excited state always involved in emission? A Comprehensive Benchmark Study
Authors: Kumar Prashant , Escudero Daniel
Published: February 2022

The reliable calculation of the phosphorescence energies of phosphor materials is at the core of designing efficient phosphorescent organic light-emitting diodes (PhOLEDs). Therefore, it is of paramount importance to have a robust computational protocol to perform those calculations in a black-box manner. In this work, we use Domain Based Local Pair Natural Orbital Coupled Cluster theory with single, double and perturbative triple excitation (DLPNO-CCSD(T)) calculations to attain the phosphorescence energies of a large pool of Pt (II) complexes. Several approaches to incorporate relativistic effects in our calculations were tested. In addition, we have used the DLPNO-CCSD(T) values (i.e., our best theoretical values) to assess the performance of different flavors of density functional theory including pure, hybrid, meta-hybrid, and range-separated functionals. Among the tested functionals, the M06HF functional provides the best values as compared with the DLPNO-CCSD(T) ones, with a mean absolute deviation (MAD) value of 0.14 eV. In its turn, and thanks to the increased accuracy achieved in the calculation of phosphorescence energies, we also demonstrate that not all the investigated complexes emit from their lowest lying triplet-state (T1). The outlier complexes include different complex photophysical scenarios and both Kasha and anti-Kasha types of complexes. Finally, we provide a general computational protocol to pre-screen whether T1 is actually the emissive state and to accurately calculate the phosphorescence energies of Pt (II) complexes.