bluuebunny/crossref_metadata_2025 huggingface dataset:
Facet-Dependent Stability of Near-Surface Oxygen Vacancies and Excess Charge Localization at CeO2 Surfaces
Authors: Pérez-Bailac Patricia , Lustemberg Pablo G. , Ganduglia-Pirovano M. Verónica
Published: February 2022

To study the dependence of the relative stability of surface (VA) and subsurface (VB) oxygen vacancies with the crystal facet of CeO2, the reduced (100), (110) and (111) surfaces, with two different concentrations of vacancies, were investigated by means of density functional theory (DFT+U) calculations. The results show that the trend in the near-surface vacancy formation energies for comparable vacancy spacings, i.e. (110) < (100) < (111), does not follow that in the surface stability of the facets, i.e. (111) < (110) < (100). The results also revealed that the preference of vacancies for surface or subsurface sites, as well as the preferred location of the associated Ce3+ polarons, are facet and concentration-dependent. At the higher vacancy concentration, the VA is more stable than the VB at the (110) facet whereas, at the (111), it is the other way around, and at the (100) facet, both the VA and the VB have similar stability. The stability of the VA vacancies, compared to that of the VB, is accentuated as the concentration decreases. Nearest neighbor polarons to the vacant sites are only observed for the less densely packed (110) and (100) facets. These findings are rationalized in terms of the packing density of the facets, the lattice relaxation effects induced by vacancy formation and the localization of the excess charge, and the repulsive Ce3+ - Ce3+ interactions.
Effect of the degree of protonation of amino acid dopants in Chirality amplification in DSCG Lyotropic Nematic phases.
Authors: Berride Fernán , Troche-Pesqueira Eduardo , Weiss Richard G. , Navarro-Vázquez Armando , Cid María Magdalena
Published: February 2022

Disodium Cromoglycate (DSCG), a lyotropic liquid crystal in water, is shown to be an amplifier of chirality when doped with small chiral molecules. Here, we study the behaviour of the DSCG nematic phase in the presence of three aminoacids with different degrees of protonation: L-Alanine, L-Arginine·HCl and L-Arginine. The results demonstrate that the sign of the helicity of the doped nematic phase (i.e., a cholesteric phase) depends on the sign of the Helical Twisting Power of the dopant.
Reversible Dissociation of a Dialumene
Authors: Falconer Rosalyn , Byrne Keelan , Nichol Gary , Krämer Tobias , Cowley Michael
Published: February 2022

Dialumenes are neutral Al(I) compounds with Al=Al multiple bonds. We report the isolation of an amidophosphine-supported dialumene. Our X-ray crystallographic, spectroscopic, and DFT computational analyses reveal a long and extreme trans-bent Al=Al bond with low dissociation energy and bond-order. In solution, the dialumene can dissociate into monomeric Al(I) species. Reactivity studies reveal two modes of reaction: as dialumene or as aluminyl monomers.
Stacked Ensemble Machine Learning for Range-Separation Parameters
Authors: Ju Cheng-Wei , French Ethan , Geva Nadav , Kohn Alexander , Lin Zhou
Published: February 2022

High-throughput virtual materials and drug discovery based on density functional theory has achieved tremendous success in recent decades, but its power on organic semiconducting molecules suffers catastrophically from self-interaction error until the optimally tuned range-separated hybrid (OT-RSH) exchange--correlation functionals were developed. The accurate but expensive fi�rst-principles OT-RSH transitions from a short-range (semi-)local functional to a long-range Hartree--Fock exchange at a distance characterized by the inverse of a molecule-specifi�c, non-empirically-determined range-separation parameter (ω). In the present study, we proposed a promising stacked ensemble machine learning model that provides an accelerated alternative of OT-RSH based on system-dependent structural and electronic con�figurations. We trained ML-ωPBE, the �first functional in our series, using a database of 1,970 organic semiconducting molecules with sufficient structural diversity, and assessed its accuracy and efficiency using another 1,956 molecules. Compared with the �first-principles OT-ωPBE, our ML-ωPBE reached a mean absolute error of 0:00504a0^{-1} for the optimal value of ω, reduced the computational cost for the test set by 2.66 orders of magnitude, and achieved a comparable predictive power in various optical properties.
Acridinone-based anion transporters
Authors: McNaughton Daniel , Macreadie Lauren , Gale Philip Alan
Published: February 2022

The arrangement of hydrogen bond donors around a central lipophilic scaffold has proven a successful strategy in the development of potent chloride transporters. In this work, we revisit an acridinone 1,9-bis(thio)urea motif which had previously shown promise as an anion sensor and expand the series of compounds by appending a variety of electron-withdrawing groups to the peripheral phenyl moieties. HIgh levels of activity were achieved by the most effective compounds in the series, which facilitated strictly electroneutral transport.
Sandacrabins – Structurally unique antiviral RNA polymerase inhibitors from a rare myxobacterium
Authors: Bader Chantal , Panter Fabian , Garcia Ronald , Tchesnokov Egor , Haid Sibylle , Walt Christine , Spröer Cathrin , Kiefer Alexander , Götte Matthias , Overmann Jörg , Pietschmann Thomas , Müller Rolf
Published: February 2022

We report structure elucidation and total synthesis of five unprecedented terpenoid-alkaloids, the sandacrabins, alongside with the first description of their producing organism Sandaracinus defensii MSr10575, which expands the Sandaracineae family by only its second member. The genome sequence of S. defensii as presented in this study was utilized to identify enzymes responsible for sandacrabin formation, whereby dimethylbenzimidazol, deriving from cobalamin biosynthesis, was identified as key intermediate. Biological activity profiling revealed that all sandacrabins except congener A exhibit potent antiviral activity against the human pathogenic coronavirus HCoV229E in the three digit nanomolar range. Investigation of the underlying mode of action discloses that the sandacrabins inhibit the SARS-CoV-2 RNA-dependent RNA polymerase complex, highlighting them as structurally distinct non-nucleoside RNA synthesis inhibitors. The observed segregation between cell toxicity at higher concentrations and viral inhibition represents a good starting point for their medicinal chemistry optimization towards selective inhibitors.
Phosphonic acid appended naphthalenediimide molecular receptor for saccharides and aminoglycoside antibiotics recognition
Authors: Nandre Kamalakar P. , Bhosale Sidhanath Vishwanath
Published: February 2022

Design of symmetric phosphonic acid functionalized naphthalene diimide bolaamphiphile (NDI 1) is reported. NDI 1 based molecular recognition of saccharides and aminoglycoside antibiotics in aqueous media was investigated. UV-vis and fluorescence measurements revealed an efficient protocol for NDI 1 as molecular receptor. The sensor successfully recognises saccharides and aminoglycoside antibiotics kanamycin and neomycin in terms of both absorbance intensity and binding affinity. This protocol provides new platform for the design and synthesis of phosphonic acid appended NDI sensor for recognition of multifunctional biomolecules.
First-Principles Plane-Wave-Based Exploration of Cathode and Anode Materials for Li and Na-ion Batteries involving Complex Nitrogen-based Anions
Authors: Ertural Christina , Stoffel Ralf P. , Müller Peter Christian , Vogt Christian Alexander , Dronskowski Richard
Published: February 2022

We present a first-principles study based on plane-wave derived Löwdin population analysis and other local bonding descriptors to investigate cathode and anode materials for lithium and sodium ion batteries, with a special emphasis on complex nitrogen chemistry. By comparing the Löwdin charges of commonly used electrode materials to other phases such as salts of dicyanamide and nanoporous carbon-based compounds, new conclusions of an improved intercalation behavior of the latter are derived. In addition, we explore the stability of the dicyanamide salts upon Li and Na removal, some of them resulting in dimerized structures. In particular, having a look at the different kinds of bonds and the corresponding covalency indicators reveals insights into the bonding changes during dimerization. Considering the astonishing thermal stability of metal dicyanamide salts, which are solid at room temperature, their electrochemical activity as well as non toxicity of alkali metal-based compounds, these materials are potential alternatives to commercially available electrodes, particularly as they show some flexibility in exhibiting anodic and cathodic behavior and allow for transition metal-free cathode materials.
Controlled sequential assembly of metal-organic polyhedra into colloidal gels with high chemical complexity
Authors: Tsang Min Ying , Tokuda Shun , Han Po-Chun , Wang Zaoming , Legrand Alexandre , Kawano Marina , Tsujimoto Masahiko , Ikeno Yuki , Urayama Kenji , Wu Kevin C.-W. , Furukawa Shuhei
Published: February 2022

Assembling many chemical components into a material in a controlled manner is one of the biggest challenges in chemistry. Particularly porous materials with multivariate character within their scaffolds are expected to demonstrate synergistic properties. In this study, we show a synthetic strategy to construct porous networks with multiple chemical components. By taking advantage of the hierarchical nature of a colloidal system based on metal-organic polyhedra (MOPs), we developed a two-step assembly process to form colloidal networks; assembling of MOPs with the organic linker to the formation of MOP network as a colloidal particle, followed by further connecting colloids by additional crosslinkers, leading to colloidal networks. This synthetic process allows not only for the use of different organic linkers for connecting MOPs and colloidal particles, respectively, but for assembling different colloidal particles formed by various MOPs. The proof-of-concept of this tuneable multivariate colloidal gel system offers an alternative to developing functional porous soft materials with multifunction.
Optimizing the dosing and trickling of nutrient media for thermophilic biomethanation in a biotrickling filter
Authors: Ashraf Muhammad Tahir , Yde Lars , Triolo Jin Mi , Wenzel Henrik
Published: February 2022

Ex-situ biomethanation in a biotrickling filter is being developed as a robust technology for the conversion of CO2 to CH4 using H2 generated from renewable power. The technology uses hydrogenotrophic methanogens in a biofilm as the catalyst and the optimum supply of nutrients in the biofilm is imperative for stable and long-term operation. In this study, essential nutrients for the methanogens in the biotrickling filter were highlighted along with a systemic investigation of the nutrient supply methods. The results showed that ammonium and iron were the critical nutrients with a minimum required concentration of 0.3 g/L and 1.5 mg/L, respectively. Furthermore, thoroughly wetting the biofilm with nutrient media, either using flooding or trickling at a high-rate, was needed to maintain an active biofilm; although, these methods temporarily reduce the conversion for a duration of 18 to 24 h due to the formation of the thicker water film.
Fluorinated Dibenzo[a,c]-phenazine-Based Green to Red Thermally Activated Delayed Fluorescent OLED Emitters
Authors: Hong Gloria , Si Changfeng , Kumar Gupta Abhishek , Bizzari Claudia , Nieger Martin , Samuel Ifor , Zysman-Colman Eli , Bräse Stefan
Published: February 2022

Purely organic thermally activated delayed fluorescence (TADF) emitting materials for organic light-emitting diodes (OLEDs) enable a facile method to modulate the emission color through judicious choice of donor and acceptor units. Amongst purely organic TADF emitters, the development of TADF molecules that emit at longer wavelengths and produce high-efficiency devices that show low efficiency roll-off remains a challenge. We report a modular synthesis route that delivers three structurally related fluorinated dibenzo[a,c]-phenazine-based TADF molecules, each bearing two donor moieties with different electron-donating strengths, namely 3,6-bis(3,6-di-tert-butyl-9H-carbazol-9-yl)-10-fluorodibenzo[a,c]phenazine (2DTCz-BP-F), 3,6-bis(9,9-dimethylacridin-10(9H)-yl)-10-fluorodibenzo[a,c]phenazine (2DMAC-BP-F) and 10,10'-(10-fluorodibenzo[a,c]phenazine-3,6-diyl)bis(10H-phenoxazine) (2PXZ-BP-F). They exhibit donor strength-controlled color-tuning over a wide color range from green to deep-red with photoluminescence maxima, PL, of 505 nm, 589 nm, and 674 nm in toluene solution. OLED devices using these TADF materials showed excellent to moderate performance with an EQEmax of 21.8% in the case of 2DMAC-BP-F, 12.4% for 2PXZ-BP-F and 2.1% with 2DTCZ-BP-F, and associated electroluminescence (EL) emission maxima, EL, of 585 nm, 605 nm and 518 nm in mCBP host, respectively.
Bandgaps of Atomically Precise Graphene Nanoribbons and Occam’s Razor
Authors: Zdetsis Aristides
Published: February 2022

Rationalization of energy gaps of atomically precise AGNRs, “bulk” (ΔΕac) or “zigzag-end” (ΔΕzz), could be challenging and controversial concerning their magnitude, origin, substrate influence (ΔΕsb), and spin-polarization, among others. Hereby, a simple self-consistent and “economical” interpretation is presented, based on “appropriate” DFT (and TDDFT) calculations, general symmetry principles, and plausibility arguments, which is fully consistent with current experimental measurements for 5-, 7-, and 9-AGNRs within less than 1%, although at variance with some prevailing views or interpretations for ΔΕac, ΔΕzz, and ΔΕsb. Thus, an excellent agreement between experiment and theory emerges, provided some established stereotypes are reconsidered and/or abandoned. The primary source of discrepancies is the finite length of AGNRs together with inversion-symmetry conflict and topological end/edge states, which invariably mix with other “bulk” states making their unambiguous detection/distinction difficult. This can be further tested by eliminating end-states (and ΔΕzz), by eliminating empty (non-aromatic) end-rings
Facile synthesis of novel heterogenous Rh/COF catalyst and its application in tandem selective transfer hydrogenation and mono-methylation of Nitro compounds with Methanol
Authors: liu Jianguo , Zhang Mingyue , Wang Nan , Wei Xiuzhi , Yang Bo , Ma Longlong
Published: February 2022

The development of transition metal heterogeneous catalysts for economical and effective synthesis of N-methylamine, especially for the mono-methylation of amines is still challenging. Herein, two unprecedented Rh-supported COFs heterogeneous catalysts Rh/MelCOF was facile synthesized by Schiff base reaction using melamine as a precursor, and for the first time, it was successfully applied to the effective and high selective tandem reaction of transfer hydrogenation and mono-methylation of nitroaromatic hydrocarbons with methanol as C1 and hydrogenation source, with water as the only by-product. A series of nitroaromatic hydrocarbons, including heterocyclic or sterically hindered derivatives, can be well tolerated and the catalyst could also be reused 4 times without losing significant reactivity. At the same time, the study of the Rh/MelCOF mechanism supports the hydrogen borrowing mechanism and puts forward the reaction pathway of azobenzene as an intermediate, which is better than the hydrogen transfer pathway from N-phenylhydroxylamine to aniline directly. This work not only expands the COF family but also provides an effective way to obtain mono N-methylated amines from nitroaromatic hydrocarbons, as well as the detailed mechanism of Rh/COF catalyzed tandem transfer hydrogenation and mono-methylation of amines.
Lignin Biorefinery Optimization Through Machine Learning
Authors: Löfgren Joakim , Tarasov Dmitry , Koitto Taru , Rinke Patrick , Balakshin Mikhail , Todorović Milica
Published: February 2022

Lignin is an abundant biomaterial that currently emerges as a low value by-product in the pulp and paper industry but could be repurposed for high-value products as part of the ongoing global transition to a sustainable society. To increase lignins value, rational and efficient approaches to optimizing lignin biorefineries to produce high value bioproducts are required. Here, we report the optimization of the AquaSolv Omni (AqSO) Biorefinery, a newly introduced biorefinery concept based on hydrothermal pretreatment and solvent extraction. We employ a machine-learning framework based on Bayesian optimization, to provide sample-efficient and guided data collection as well as surrogate model building. The surrogate models allow us to map multiple experimental outputs, including the extracted lignin yield and main structural properties obtained by 2D NMR, as functions of the hydrothermal pretreatment reaction severity and temperature. Our results show that with Bayesian optimization, predictive models can be converged with only 21 data points to within a margin of error comparable to the underlying experimental error. By applying a Pareto point analysis, we demonstrate how the predictive models can be used in tandem to identify optimal extraction conditions for concrete applications in lignin valorization.
Long-range interactions boost singlet exciton diffusion in nanofibers of $\pi$-extended polymer chains
Authors: Prodhan Suryoday , Giannini Samuele , Wang Linjun , Beljonne David
Published: February 2022

Raising the distance covered by singlet excitons during their lifetimes to values maximizing light absorption (a few hundred nm) would solve the exciton diffusion bottleneck issue and lift the constraint for fine (~10 nm) phase segregation in bulk heterojunction organic solar cells. In that context, the recent report of highly ordered conjugated polymer nanofibers featuring singlet exciton diffusion length, $L_D$, in excess of 300 nm is both appealing and intriguing [X. Jin et al., Science 360, 897 (2018)]. Here, on the basis of non-adiabatic molecular dynamics simulations, we demonstrate that singlet exciton diffusion in poly(3-hexylthiophene) (P3HT) fibers is highly sensitive to the interplay between delocalization along the polymer chains and long-range interactions along the stacks. Remarkably, the diffusion coefficient is predicted to rocket by three orders of magnitude when going beyond nearest-neighbor intermolecular interactions in fibers of extended (30-mer) polymer chains and to be resilient to interchain energetic and positional disorders.
The Orbital Origins of Chemical Bonding in Phase-Change Materials
Authors: Hempelmann Jan , Müller Peter C. , Ertural Christina , Dronskowski Richard
Published: February 2022

Layered phase-change materials in the Ge–Sb–Te-system are widely used in data storage and are the subject of intense research to understand the elusive quantum-chemical origin of their unique properties. To uncover the nature of the underlying periodic wavefunction, we study the interacting atomic orbitals including their phase information as revealed by crystal orbital bond index (COBI) and fragment crystal orbital (FCO) analysis. In full accord with previous and also new findings based on projected force constants (pFC), we demonstrate the decisive role of multicenter bonding along straight atomic connectivities such as Te–Ge–Te and Te–Sb–Te. While the here found multicenter bonding resembles well-established three-center four-electron bonding in molecules, its solid-state manifestation beyond a molecular motif leads to distinct longe-range consequences, thus serving to contextualize the aforementioned material properties usually termed “metavalent”. For example, we suggest multicenter bonding to be the origin of their astonishing bond-breaking and also phase-change behavior. As a hole-in-one, multicenter bonding immediately explains the too small “van der Waals” gaps between individual layers since multicenter bonding forces these gaps to shrink below the nonbonding Te–Te distances.
Molecular persistent luminescence imaging with porphyrin derivatives for ultrasensitive image-guided cancer surgery and drug screening
Authors: Duan Xingchen , Zhang Guoqiang , Ji Shenglu , Zhang Yiming , Li Jun , Ou Hanlin , Gao Zhiyuan , Feng Guangxue , Ding Dan
Published: February 2022

Persistent luminescence without excitation light and tissue autofluorescence interference holds great promise for in vivo imaging and sensing. However, the availability of persistence luminescence materials is largely limited by potential toxicity, instability, short-wavelength emissions, and poor clinical potential for currently available ones. Here we report a series of porphyrin derivatives with near-infrared (NIR) persistence luminescence for image-guided cancer surgery and drug screening. These porphyrin derivatives showed NIR persistence luminescence over 760 nm after cessation of excitation light or upon interaction with peroxynitrite (ONOO-), and a plausible mechanism of ordered oxidation of vinylene bond is proposed. Through molecular engineering with adaptive peptides bearing the functions of β-sheet-formatting and cancer cell targeting, the resultant Ppa-FFGYSA supermolecular probe showed enhanced photoacoustic and persistence luminescence signals, facilitating preoperative photoacoustic tumor identification and intraoperative persistence luminescence image-guided tumor resection with outperformed signal-to-background ratio. In addition, the activated persistence luminescence in recognition of ONOO- also permits the specific monitoring of neutrophil infiltration and screening of immunogenic cell death (ICD) drugs with high sensitivity and specificity.
Immobilized cellulose nanospheres in lateral flow immunoassay enable rapid nucleocapsid antigen-based diagnosis of SARS-CoV-2 from salivary samples
Authors: Solin Katariina , Beaumont Marco , Borghei Maryam , Orelma Hannes , Mertens Pascal , Rojas Orlando J.
Published: February 2022

Rapid and efficient diagnostic systems are essential in controlling the spread of viral pathogens and efficient patient management. The available technologies for low-cost viral antigen testing have several limitations, including lack of accuracy and sensitivity. Here, we develop sensitive antigen tests based on recently introduced, oppositely charged cellulose II nanoparticles (NPan and NPcat) that are effective in controlling surface protein interactions. Passivation against non-specific adsorption and augmented immobilization of sensing antibodies are achieved by adjusting the electrostatic charge of the nanoparticles. The interactions affecting the performance of the system are investigated by microgravimetry and confocal imaging. We further demonstrate SARS-CoV-2 nucleocapsid rapid sensing by saliva-wicking channels stencil-printed on flexible paper supports. Therein, NPcat inkjet printed on the channels elicit distinctive optical signals, visible after only a few minutes, allowing faster diagnosis compared to current microfluidic devices designed for saliva sampling.
The Structure and Dynamics of the NaOH(aq):Gibbsite Interface
Authors: Liu Wei , Pouvreau Maxime , Stack Andrew , Yang Xiaoning , Clark Aurora
Published: February 2022

Gibbsite (γ-Al(OH)3) is one of the primary mineral structures containing Al, and its interfacial chemistry in NaOH(aq) solutions is relevant to the industrial processing of aluminum, including metal production and the disposition of Al-containing wastes. To date, little is known about the structure, speciation, and dynamic behavior of gibbsite interfaces with NaOH(aq)—particularly as a function of ionic strength. Yet this is critical in order to understand interfacial reactivity, including dissolution mechanisms and rates that underpin industrial Al processing. This work reports equilibrium molecular dynamics simulations of the γ-Al(OH)3:NaOH(aq) interface, revealing the sorption behavior and speciation of ions from 0.5 – 10 M [NaOH]. As inner-sphere complexes, Na+ primarily coordinates to the side of the gibbsite hexagonal cavities, while OH- accepts hydrogen-bonding from the surface -OH groups. The mobility of inner-sphere Na+ and OH- ions is obviously reduced due to the strong surface affinity. At high [NaOH], ion pairing that is observed in the bulk solution is partially disrupted upon sorption to the gibbsite surface by the individual ion-surface interactions. We anticipate that surface ion-pairing is a key element of the dissolution mechanism and that its modulation (by considering concentration and different ion combinations) may be used to tune gibbsite interfacial chemistry.
Reaction on a Rink: Kondo-Enhanced Heterogeneous Single-atom Catalysis
Authors: Li Xiangyang , Gong Hong , Zhuang Qingfeng , Wang Bing , Zheng Xiao , Yang Jinlong
Published: February 2022

Boosting the efficiency of heterogeneous single-atom catalysts (SACs) by adjusting the microenvironment of the active atom has recently attracted enormous attention. However, attempts to tune the spin-spin interaction between the SAC and its microenvironment have remained rather scarce. Some interesting questions can be raised, among which a fundamental one is: can the surrounding environment influence the local spin state of an SAC, and if so, can such influence be utilized to enhance the catalytic activity? In this work, we explore such a possibility by investigating the thermochemical effect of Kondo screening of a local atomic spin by free electrons in the metal support. Inspired by the exothermicity of the spin-screening interaction, a novel approach to heterogeneous catalysis -- reaction on a rink (ROAR) -- is proposed. In contrast to the conventional notion of thermal catalytic reaction, lowering the temperature of metal support is predicted to result in a reduced reaction barrier. As a proof of concept, CO oxidation catalyzed by the Co@CoPc/Au(111) composite is scrutinized. By combining the density functional theory and a hierarchical equations of motion approach, it predicts that the existing s-d hybridization between the magnetic d orbital of Co adatom and the substrate metallic states in the transition state will lower the free energy barrier and accelerate the reaction rate. Furthermore, if the strength of s-d hybridization is enlarged, a more appreciable speedup will be achieved. This work highlights the potential usefulness of the spin degrees of freedom to heterogeneous single-atom catalysis, and our proposed ROAR approach could open up a new horizon for exploiting the role of atomic spin in chemical reactions.
Direct Seawater Electrolysis via Synergistic Acidification by Inorganic Precipitation and Proton Flux from Bipolar Membrane
Authors: Han Ji-Hyung , Jwa Eunjin , Lee Hongjun , Kim Eun Joong , Nam Joo-Youn , Hwang Kyo Sik , Jeong Namjo , Choi Jiyeon , Kim Hanki , Jeung Youn-Cheul , Chung Taek Dong
Published: February 2022

This report describes direct seawater electrolysis (DSE) wherein natural seawater is used as a catholyte without filtration or pretreatment; seawater is acidified to a pH of 2 while hydroxide ions are produced at the cathode by the hydrogen evolution reaction (HER). It results from the cooperative effect of hydroxide ions trapped through inorganic precipitation at the cathode and proton flux from water dissociation in a bipolar membrane (BPM; used as a separator). The acidification of the catholyte in the proposed BPM-DSE substantially mitigates cathode passivation, eliminates the requirement of additional processes for treatment of inorganic precipitates dispersed in the catholyte, and reduces the cathode potential (𝐸𝑐) required for the HER to enable long-term DSE. The BPM in this system plays a critical role in maintaining the electrolyte concentration, suppressing the chlorine evolution reaction (ClER), and maximizing the oxygen evolution reaction. These findings are expected to suggest a breakthrough toward large-scale operation of DSE that successfully overcomes challenges such as energy consumption, inorganic precipitation, ClER, and corrosion.
Into the Facet-Selectivity of Sequenced Amphiphilic Peptoids at the Au-Water Interface
Authors: Qi Xin , Jin Biao , Cai Bin , Yan Feng , De Yoreo James , Chen Chun-Long , Pfaendtner Jim
Published: February 2022

Shape-controlled colloidal nanocrystal syntheses often require aid from facet-selective solution-phase chemical additives to regulate atom addition/migration fluxes or oriented particle attachment. Because of their highly tunable chemical property and robustness to a wide range of experimental conditions, peptoids contribute to a very promising group of next-generation functional chemical additives. To generalize the design philosophy, it is critical to understand the origin of facet selectivity at the molecular level. We employ molecular dynamics simulations and biased sampling methods to investigate the origin of Au(111)-favored adsorption of a peptoid, Nce3Ncp6, that is evidenced to assist the formation of five-fold twinned nanostructures. We find that the facet-selectivity is achieved through a synergistic effect of both molecule-surface and solvent-surface interactions. Extending beyond the single-chain scenario, the order of peptoid-peptoid and peptoid-surface energetics, i.e., peptoid-Au(100) < peptoid-peptoid < peptoid-Au(111), further amplifies the distinct behavior of Nce3Ncp6 chains on different Au surfaces. Our studies set the stage for future peptoid design in shape-controlled nanocrystal syntheses by probing the facet selectivity from various perspectives.
The behavior of triplet thymine in a model B-DNA strand. Energetics and spin density localization revealed by ab initio molecular dynamics simulations.
Authors: Allahkaram Laleh , MONARI Antonio , Dumont Elise
Published: February 2022

Among the natural occurring nucleobases, thymine presents the lowest triplet state, hence it represents a hotspot for energy transfer and photosensitization. In turn, the population of the triplet state may lead to thymine dimerization and hence to the production of toxic DNA lesions and has been the subject of intensive theoretical and experimental investigations. Relying on QM/MM molecular dynamics simulations, we have sought to situate the energy of the lowest triplet state of thymine embedded in a B-DNA environment. The energy gap varies between 305 and 329 kJ.mol−1 when a single thymine is treated at the quantum chemistry level, depending on its position in the model double-stranded 16-bp oligonucleotide. The energy of triplet state decreases up to 300 kJ.mol−1, due to polarization effects, when we consider coupled stacked nucleobases up to the inclusion of four nucleobases. Our value lies in good agreement with the energy inferred experimentally by Miranda and coworkers (270 kJ.mol−1), and our theoretical exploration opens the door to investigations toward other more complex and biological relevant environments, such as thymines embedded in nucleosome core particles. Our investigations also provide a reference for further studies using semiempirical approaches such as density functional based tight binding, allowing to further rationalize sequence effects.
Recognition of Aloe vera compounds as potential inhibitors of SARS-CoV-2 NSP-16: Molecular docking approach for drug development
Authors: Shaji Divya , Das Abhinav
Published: February 2022

Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV-2) is a rapidly spreading virus that appeared at the end of 2019 in Wuhan, China. To date, there is no effective treatment for COVID-19. Aloe vera is a widely used medicinal plant and its antiviral activities are well documented. A molecular docking approach was employed in this study to identify the drug lead compounds from Aloe vera against SARS-CoV-2 Non-Structural Protein 16 (NSP-16). A set of 14 Aloe vera compounds satisfying ‘Lipinsky’s rule of five’ was collected from the literature. The results suggested that compounds feralolide, aloe-emodin, eupatorin, aloesaponarinII, chrysophanol and aloesaponarinI can bind strongly to the active site of NSP-16, and can be promising natural candidates to inhibit NSP-16.
Trapping the Transition State in a [2,3]-Sigmatropic Rearrangement by Applying Pressure
Authors: Kumar Sourabh , Stauch Tim
Published: February 2022

Transition states are of central importance in chemistry. While they are, by definition, transient species, it has been shown before that it is possible to “trap” transition states by applying stretching forces. We here demonstrate that the task of transforming a transition state into a minimum on the potential energy surface can be achieved by using hydrostatic pressure. We apply the computational eXtended Hydrostatic Compression Force Field (X- HCFF) approach to the educt of a [2,3]-sigmatropic rearrangement in both static and dynamic calculations and find that the five-membered cyclic transition state of this reaction becomes a minimum at pressures in the range between 100 and 150 GPa. Slow decompression leads to a 70:30 mix of the product and the educt of the sigmatropic rearrangement. Our findings are discussed in terms of geometric parameters and electronic rearrangements throughout the reaction. We speculate that the trapping of transition states by using pressure is generally possible if the transition state of a chemical reaction has a more condensed geometry than both the educt and the product, which paves the way for new ways of initiating chemical reactions.
Rapid Design, Fabrication, and Optimization of 3D Printed Photonic Topological Insulators
Authors: Sabatini Mattei Michael , Liu Boyuan , Mazzei Capote Gerardo A. , Liu Zijie , Osswald Tim A. , Yu Zongfu , Goldsmith Randall H.
Published: February 2022

Photonic topological insulators have emerged as an exciting new platform for backscatter-free waveguiding even in the presence of defects, with applications in robust long-range energy and quantum information transfer, low-threshold lasing, and chiral quantum optics. We demonstrate a design for spin-Hall photonic topological insulators with remarkably low refractive index contrast, enabling the synthesis of photonic topological waveguides from polymeric materials for the first time. Our design is compatible with additive manufacturing methods, including fused filament fabrication, and constitutes the first demonstration of a 3D printed photonic topological insulator. We combine rapid device fabrication through 3D printing with high-speed FDTD simulation to showcase an iterative design cycle capable of screening thousands of device configurations with unprecedented speed. We have identified and experimentally verified a non-intuitive geometry for bent topological waveguides with optimized transmission. Our rapid design cycle represents a powerful new tool set for designing, optimizing, and synthesizing photonic topological materials.
A quadruplex-DNA binder functionalised with a SPECT probe for in vivo imaging
Authors: Lo Rainbow , Fruhwirth Gilbert , Vilar Ramon
Published: February 2022

Guanine-rich sequences of DNA can fold into intramolecular tetra-helical assemblies known as G-quadruplexes (G4). Their formation in vivo has been associated to a range of biological functions and therefore they have been identified as potential drug targets. Consequently, a broad range of small molecules have been developed to target quadruplexes. However, to date, there is very limited information of the biodistribution of quadruplex binders in whole organisms. Here, we report the functionalisation of a well-established G4 DNA binder (based on a square planar platinum(II)-salphen complex) with two different radiolabelled complexes. An 111In-conjugate was successfully used to assess its in vivo distribution in a mouse tumour model using single-photon emission computed tomography (SPECT) imaging. These studies have shown the overall biodistribution of the G4 DNA binder highlighting its accumulation in the tumour.
Liquid water simulation using hydrogen bond corrected SCAN and neural network potentials.
Authors: Duignan Timothy
Published: February 2022

Accurately reproducing the structure of liquid water with ab initio molecular dynamics (AIMD) simulation is a crucial first step on the path towards accurately predicting the properties of liquid solutions without relying on experiment. Density functional theory (DFT) is normally used to approximate the forces in these simulations. However, no DFT functional has been shown to give an entirely satisfactory description of the structure of liquid water. Here, I propose a simple correction to the strongly constrained and appropriately normalised (SCAN) DFT functional, that corrects the strength of the hydrogen bonding interaction with a simple exponential potential fitted to dimer energy calculations. The resulting SCAN-CH functional provides an excellent description of the structure of liquid water. Long time scale NPT simulations are enabled by the use of neural network potentials, which demonstrate that the simulations are well converged and that the density of water is also more accurately reproduced with this method.
CRISPR-Click Enables Multi-Gene Editing with Modular Synthetic sgRNAs
Authors: Park Hansol , Osman Eiman , Cromwell Christopher , St. Laurent Christopher , Liu Yuning , Kitova Elena , Klassen John , Hubbard Basil , Macauley Matthew , Gibbs Julianne
Published: February 2022

Gene editing systems such as CRISPR/Cas9 readily enable individual gene phenotypes to be studied through loss-of-function. However, in certain instances, gene compensation can obfuscate the results of these studies, necessitating the editing of multiple genes to properly identify biological pathways and protein function. Performing multiple genetic modifications in cells remains difficult due to the requirement for multiple rounds of gene editing. While fluorescently labeled guide RNAs (gRNAs) are routinely used in laboratories for targeting CRISPR/Cas9 to disrupt individual loci, technical limitations in single guide RNA (sgRNA) synthesis hinder the expansion of this approach to multi-color cell sorting. Here, we describe a modular strategy for synthesizing sgRNAs where each target sequence is conjugated to a unique fluorescent label, which enables fluorescence-assisted cell sorting (FACS) to isolate cells that incorporate the desired combination of gene-editing constructs. We demonstrate that three short strands of RNA functionalized with strategically placed 3’-azide and 5’-alkyne terminal deoxyribonucleotides can be assembled in a one-step, template-assisted, copper-catalyzed alkyne-azide cycloaddition (CuAAC) to generate fully functional, fluorophore-modified sgRNAs. Using these synthetic sgRNA in combination with FACS, we achieved selective cleavage of two targeted genes, either separately as a single color experiment or in combination as a dual-color experiment. These data indicate that our strategy for generating doubly-clicked sgRNA allows for Cas9 activity in cells. By minimizing the size of each RNA fragment to 41 nucleotides or less, this strategy is well suited for custom, scalable synthesis of sgRNAs.
High-entropy intermetallics serve an ultrastable single-atom Pt for propane dehydrogenation
Authors: Nakaya Yuki , Hayashida Eigo , Asakura Hiroyuki , Shimizu Ken-ichi , Furukawa Shinya
Published: February 2022

Propane dehydrogenation (PDH) has been a promising propylene production process that can compensate for the increasing global demand for propylene. However, Pt-based catalysts with high stability at ≥600°C have barely been reported because the catalysts typically result in short catalyst life owing to side reactions and coke formation. Herein, we report a new class of heterogeneous catalysts using high-entropy intermetallics (HEIs). Pt–Pt ensembles, which cause side reactions, are entirely diluted by the component inert metals in PtGe-type HEI; thereby, unfavorable side reactions are drastically inhibited. The resultant HEI: (PtCoCu)(GeGeSn)/Ca–SiO2 exhibited an outstandingly high catalytic stability, even at 600°C (kd−1 = τ = 4146 h = 173 d), and almost no deactivation of the catalyst was observed two months for the first time.
Highly selective synthesis of citronellal in water at multigram scale by Pd nanoparticles-catalyzed hydrogenation of citral
Authors: Marion DUVAL , Gilles SAGORIN , Denicourt-Nowicki Audrey , ROUCOUX Alain
Published: February 2022

The synthesis of citronellal, an added-value chemical for perfumery, was carried out by selective and green hydrogenation of citral into citronellal in water. Aqueous suspensions of spherical ammonium-capped palladium nanoparticles with sizes around 3nm selectively reduced the conjugated carbon-carbon double bond. An excellent selectivity of 95% in citronellal was achieved at complete conversion under mild reaction conditions on a realistic 2 g scale in water. The presence of potassium hydroxide proved crucial to control the selectivity and avoid other hydrogenation co-products. These optimized results were further extended to a 135 g substrate loading with a relevant turnover number (TON) of 10 000.
Herzberg-Teller Vibronic Coupling Effect on the Vibrationally-Resolved Electronic Spectra and Intersystem Crossing Rates of a TADF Emitter: 7-PhQAD
Authors: Lin Sirong , Pei Zheng , Zhang Bin , Ma Huili , Liang Wanzhen
Published: February 2022

Assessing and improving the performance of organic light-emitting diode (OLED) materials require quantitative prediction of rate coefficients for the intersystem crossing (ISC) and reverse ISC (RISC) processes, which are determined not only by the singlet-triplet energy gap and the direct spin-orbit coupling (SOC) at a thermal equilibrium position of the initial electronic state but also by the non-Condon effects such as the Herzberg-Teller vibronic coupling (HTVC) and the spin-vibronic coupling (SVC). Here we applied the time-dependent correlation function approaches to calculate the vibronic absorption and fluorescence spectra and ISC and RISC rates of a newly synthesized multiple-resonance-type (MR-type) thermally activated delayed fluorescence (TADF) emitter, 7-phenylquinolino[3,2,1-de]acridine-5,9-dione (7-PhQAD), with inclusion of the Franck-Condon (FC), HTVC, and Duschinsky rotation effects. It is found that the experimentally-measured ISC rate of 7-PhQAD originates predominantly from the HTVC which increases the ISC rate by more than one order of magnitude while the HTVC effect on the vibronic spectra is negligible. The small discrepancy between the theoretical and experimental rates originates from the neglect of the second-order SVC and the inaccurate excited states calculated by the single-reference time-dependent density functional theory. This work provides a demonstration of what proportion of ISC and RISC rate coefficients of a MR-type TADF emitter can be covered by the contribution of HTVC, and opens design routes that go beyond the FC approximation for the future development of high-performance systems.
Denatured crude protein extracts from the sea anemone Entacmaea quadricolor as capping agents for silver nanoclusters
Authors: Espiritu Rafael , Chu Jasmin
Published: February 2022

Novel nanomaterials derived from numerous biological samples including extracts from plants, animals, and even bacteria have gained prominence due to their unique properties, more environmental friendly preparation, and interesting bioactivities. Among these, protein-capped noble metal, e.g., Ag, nanoclusters (NC) have gained considerable attention for their many potential applications, and significant efforts are being directed at using a wide variety of protein sources as capping agents as well as. In this work, crude protein extracts from the sea anemone Entacmaea quadricolor (E. quadricolor) subjected to either heat or β-mercaptoethanol denaturation were prepared to investigate the effects of these processes in the formation of AgNC and on its preliminary bioactivity, measured using a hemolysis assay against human erythrocytes. Fourier-transform infrared spectrometry (FTIR) analysis showed comparable spectra for the two denatured crude protein-capped AgNC, as well with as the undenatured protein-capped AgNC, like previous reports indicating successful capping of the NC. Moreover, the spectra suggest no significant alterations if protein secondary structure upon NC formation. The crude protein extracts were also found to be very weakly hemolytic at the concentration range tested (0.5 – 1 mg protein/mL) and denaturing the protein prior to NC formation did not significantly alter its hemolytic activity as well. These results imply that E. quadricolor crude protein denaturation prior to use with the reduction of Ag+ has no deleterious effects in functioning as capping agents for the prepared AgNC.
Reduction of Sulfur Dioxide to Sulfur Monoxide by Ferrous Porphyrin
Authors: Bhattacharya Aishik , Nath Arnab , Ghatak Arnab , Nayek Abhijit , Saha Rajat , Dey Somdatta , Dey Abhishek
Published: February 2022

Reduction of SO¬2 to fixed forms of sulfur can address the growing concerns regarding its detrimental effect on health and environment as well as enable its valorization into valuable chemicals. While the coordination of SO2 to transition metals are documented, its reduction using molecular catalysts has remained elusive. Alternatively, the naturally occurring heme en-zyme sulfite reductase is known to reduce SO2 to H2S and is an integral part of the global sulfur cycle. However, its action is not yet mimicked in artificial systems outside of the protein matrix even after several decades of its structural elucidation. Here reduction of SO2 by iron (II) porphyrin, a synthetic analogue of heme, is demonstrated. A combination of spectroscop-ic and analytical methods indicates that SO2 is reduced by 2e-/2H+ by FeIITPP to form an intermediate [FeIII-SO]+ species which releases SO. The SO obtained from the chemical reduction of SO2 could be valorized in the form of a Diels-Alder ad-duct of butadiene resulting in an organic sulfoxide.
Design, Synthesis, and Evaluation of Trivalent PROTACs Having a Functionalization Site with Controlled Orientation
Authors: Huang Yifan , Yokoe Hiromasa , Kaiho-Soma Ai , Takahashi Kazunori , Hirasawa Yusuke , Morita Hiroshi , Ohtake Fumiaki , Kanoh Naoki
Published: February 2022

Trivalent PROTACs having a functionalization site with controlled orientation were designed, synthesized, and evaluated. Based on the X-ray structure of BRD protein degrader MZ1 (1) in complex with human VHL and BRD4BD2, we expected that the 1,2-disubstituted ethyl group near the JQ-1 moiety in MZ1 (1) could be replaced by a planar benzene tether as a platform for further functionalization. To test this hypothesis, we first designed six divalent MZ1 derivatives, 2a-c and 3a-c, by combining three variations of substitution patterns on the benzene ring (1,2-, 1,3-, and 1,4-substitution) and two variations in the number of ethylene glycol units (1 or 2). We then tested the synthesized compounds for the BRD4 degradation activity of each. As expected, we found that 1,2D-EG2-MZ1 (2a), an MZ1 derivative with 1,2-disubstituted benzene possessing two ethylene glycol units, had an activity profile similar to that of MZ1 (1). Based on the structure of 2a, we then synthesized and evaluated four isomeric trivalent MZ1 derivatives, 15a-15d, having a tert-butyl ester unit on the benzene ring as a handle for further functionalization. Among the four isomers, 1,2,5T-EG2-MZ1 (15c) retained a level of BRD4 depletion activity similar to that of 2a without inducing a measurable Hook effect, and its BRD4 depletion kinetics was the same as that of MZ1 (1). Other isomers were also shown to retain BRD4 depletion activity. Thus, the trivalent PROTACs we synthesized here may serve as efficient platforms for further applications.