bluuebunny/crossref_metadata_2025 huggingface dataset:
Icosahedral Meta-Carboranes Containing Exopolyhedral B-Se and B-Te Bonds
Authors: Mills Harrison , Alsarhan Fadi , Ong Ta-Chung , Gembicky Milan , Rheingold Arnold , Spokoyny Alexander
Published: February 2022

Chalcogen-containing carboranes have been known for several decades and possess stable exopolyhedral B(9)-Se and B(9)-Te σ bonds despite the electron-donating ability of the B(9) vertex. While these molecules are known, little has been done to thoroughly evaluate their electrophilic and nucleophilic behavior. Herein, we report an assessment of the electrophilic reactivity of meta-carboranyl selenyl (II), tellurenyl (II), and tellurenyl (IV) chlorides and establish their reactivity pattern with Grignard reagents, alkenes, alkynes, enolates, and electron-rich arenes. These electrophilic reactions afford unique electron-rich B-Y-C (Y = Se, Te) bonding motifs not commonly found before. Furthermore, we show that meta-carboranyl selenolate, and even meta-carboranyl tellurolate, can be competent nucleophiles and participate in nucleophilic aromatic substitution reactions. Arene substitution chemistry is shown to be further extended to electron-rich species via the palladium mediated cross-coupling chemistry.
Si-doped Polycyclic Aromatic Hydrocarbons: Synthesis and Opto-electronic Properties
Authors: Delouche Thomas , Taifour Ghizlene , cordier Marie , Roisnel Thierry , Tondelier Denis , Manzhi Payal , Geffroy Bernard , Le Guennic Boris , Jacquemin Denis , Hissler Muriel , Bouit Pierre-Antoine
Published: February 2022

We report the straightforward synthesis of Si-containing PAHs. The impact of pi-extension and exocyclic modifications on both the optical and redox properties is investigated using a joint experimental/theoretical approach. By taking advantage of the solid-state luminescence of these derivatives, electroluminescent devices are prepared. Such preliminary optoelectronic results highlight that these heteroatom-containing PAHs are promising building blocks for organic electronics.
A microbial sulfoquinovose monooxygenase pathway enables sulfosugar assimilation
Authors: Sharma Mahima , Lingford James , Petricevic Marija , Snow Alexander , Zhang Yunyang , Jarva Michael , Mui Janice , Scott Nichollas , Saunders Eleanor , Mao Runyao , Epa Ruwan , da Silva Bruna , Pires Douglas , Ascher David , McConville Malcolm , Davies Gideon , Williams Spencer , Goddard-Borger Ethan
Published: February 2022

Breakdown of the sulfosugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose), produced by photosynthetic organisms, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a new pathway for SQ degradation involving oxidative desulfurization to release sulfite and complete breakdown of the carbon skeleton of this sugar to support the growth of the plant pathogen Agrobacterium tumefaciens. SQ or its glycoside sulfoquinovosyl glycerol are imported by an ABC transporter system with associated SQ binding protein. A sulfoquinovosidase cleaves the SQ glycoside and a flavin mononucleotide-dependent sulfoquinovose monooxygenase acts in concert with an NADH-dependent flavin reductase to release sulfite and form 6-oxo-glucose. A short-chain dehydrogenase/reductase oxidoreductase reduces 6-oxo-glucose to glucose, allowing it to enter primary metabolism. Structural and biochemical studies provide detailed insights into the binding and recognition of key species along the reaction coordinate. This sulfoquinovose monooxygenase pathway is distributed across alphaproteobacteria and especially within the rhizobiales. This metabolic strategy...
A Computationally-Realizable Rigorous Canonical Numbering Algorithm for Chemical Graphs with its Open-Source Implementation in Rust
Authors: Wan Qin
Published: February 2022

Canonical numbering of the vertices from a graph has been a challenging open issue for decades not only in the domain of graph theory but also in the cheminformatic applications. This paper presents an efficient, fast and rigorous approach for canonical numbering and symmetry perception as the first workable solution with theoretical completeness. The methodology is composed of a set of algorithms including extendable representation of vertex, high-performance sorting and graph reduction, etc. The canonical numbering of vertices can be generated in a short time through the novel vertex representation method. Furthermore, a new concept of graph reduction decreases the amount of computation to determine constitutional symmetry of complex graphs into the range of hardware capability. An open-source version of algorithms overall is implemented in Rust thanks to the features of safety, performance and robust abstraction of this modern programming language. The results of experiments on more than 2 million molecules from ChEMBL database has been given at the end.
Localized Quantum Chemistry on Quantum Computers
Authors: Otten Matthew , Hermes Matthew , Pandharkar Riddhish , Alexeev Yuri , Gray Stephen , Gagliardi Laura
Published: February 2022

Quantum chemistry calculations of large, strongly correlated systems are typically limited by the computation cost that scales exponentially with the size of the system. Quantum algorithms, designed specifically for quantum computers, can alleviate this, but the resources required are still too large for today’s quantum devices. Here we present a quantum algorithm that combines a localization of multireference wave functions of chemical systems with quantum phase estimation (QPE) and variational unitary coupled cluster singles and doubles (UCCSD) to compute their ground state energy. Our algorithm, termed “local active space unitary coupled cluster” (LAS-UCC), scales linearly with system size for certain geometries, providing a polynomial reduction in the total number of gates compared with QPE, while providing accuracy above that of the variational quantum eigensolver using the UCCSD ansatz and also above that of the classical local active space self-consistent field. The accuracy of LAS-UCC is demonstrated by dissociating (H2)2 into two H2 molecules and by breaking the two double bonds in trans-butadiene and resources estimates are provided for linear chains of up to 20 H2 molecules.
THE VARIABILITY OF VOLATILE ORGANIC COMPOUNDS IN CLINICAL ENVIRONMENTS
Authors: Salman Dahlia , Ibrahim Wadah , Kanabar Amisha , Zhao Bo , Singapuri Amisha , Wilde Michael , Cordell Rebecca , McNally Teresa , Ruszkiewicz Dorota , Hadjithekli Andria , Free Robert , Greening Neil , Gaillard Erol , Beardsmore Caroline , Monks Paul , Brightling Christopher , Siddiqui Salman , Thomas Charles
Published: February 2022

The development of clinical breath-analysis is confounded by the variability of background volatile organic compounds (VOC). Interpretation of clinical breath-data at individual, and cohort levels requires characterisation of clinical-VOC levels and exposures. Active-sampling with thermal-desorption/gas chromatography-mass spectrometry recorded and evaluated VOC concentrations in 245 samples of indoor air from three sites in a large NHS provider trust in the UK over 27 months. 7344 clinical VOC were isolated and 328 VOC and 68 were observed in more than 5% and 30% of samples respectively; associated with exogenous and endogenous sources. 17 VOC were seasonal differentiators. Metabolites from the anaesthetic sevoflurane, and putative-disease biomarkers in room air indicated that exhaled VOC were a source of background-pollution in clinical breath-tests. Apart from solvents, and PPE-waxes, exhaled VOC concentrations above 3 µgm-3 are unlikely to arise from room air contamination. This level could be applied as a threshold for inclusion in studies.
Transfer C-H Borylation of Alkenes under Rh(I)-Catalysis: In-sight into the Mechanism, Selectivity-Control & Synthetic Capacity
Authors: Dydio Pawel , Veth Lukas , Grab Hanusch , Martinez Sebastian , Antheaume Cyril
Published: February 2022

Transfer C-H borylation of alkenes bears the potential to unlock a range of attractive transformations for modular synthe-sis and late-stage derivatization of complex molecules. However, its scarce precedence associated with a limited mechanistic understanding hinders the development of practical synthetic protocols. Here we report a Rh(I)-catalyzed transfer C-H borylation reaction that is founded on an unprecedented yet crucial elementary step of the beta-boryl elimination engaging the Rh(I)-(beta-borylalkyl) intermediate. A thorough mechanistic investigation involving a series of catalytic and stoichiometric experiments and complementary computational studies revealed that this step proceeds with a considerably low free energy barrier, further elucidated the full catalytic cycle, and provided insight into the features con-trolling the activity and the selectivity. Driven by this mechanistic understanding, we devised a protocol that is compatible with a plethora of functional groups, including often problematic motifs, and applicable not only to terminal but also inter-nal alkenes and varied electronic and steric properties. The method proved also to be effective in complex settings of the late-stage borylation of derivatives of macrocyclic mycoestrogen Zearalenol, bioactive Brompheniramine, Chlorpromazine, and CD3254, and the synthesis of the boronic acid bio¬isostere of the drug Ozagrel. Besides the valuable new method, these mechanistic investigations set the stage for the development of other hydrogen-for-functional group exchange reactions undergoing a similar pathway.
Light sensitive phenacyl crosslinked dextran hydrogels for controlled delivery
Authors: Eelkema Rienk , Denkova Antonia , Breve Tobias , Weerdenburg Sven , van der Griend Stefan , Groeneveld Tim , Filius Mike
Published: February 2022

Stimuli-responsive soft materials enable controlled release of loaded drug molecules and biomolecules. Controlled release of potent chemotherapeutic or immunotherapeutic agent is crucial to reduce unwanted side effects. In an effort to develop controlled release strategies that can be triggered using Cerenkov luminescence, we have developed polymer hydrogels that can release doxorubicin, bovine serum albumin and immunoglobulin G using light (254 nm – 375 nm) as a trigger. We describe the synthesis and photochemical characterisation of two light sensitive phenacyl bis-azide crosslinkers that are used to prepare transparent self-supporting hydrogel patches. One crosslinker was designed to optimize the overlap with the Cerenkov luminescence emission window, bearing an -extended phenacyl core, resulting in a high quantum yield (14%) of photocleavage when irradiated with 375 nm light. We used the extended phenacyl crosslinker for the preparation of protein-loaded dextran hydrogel patches, which showed efficient and selective dosed release of bovine serum albumin or immunoglobulin G after irradiation with 375 nm light. Based on the high quantum yield, efficient release and large overlap with the Cerenkov window, we envision application of these photosensitive soft materials in radiation targeted drug release.
Boosting Palladium Catalyzed Aryl–Nitro Bond Activation Reaction by Understanding the Electronic, Electrostatic and Polarization Effect: A Computational Study from Basic Understanding to Ligand Design
Authors: Ma Yumiao , Wang Zhaohong
Published: February 2022

Although cross coupling reaction with nitroarene as the electrophilic partner has gained high interest recently, the palladium catalyzed aryl–nitro bond activation reaction still requires rather high temperature and hash condition. In this work, based on Nakao’s nitrogen heterocyclic carbene (NHC) ligand, we systematically explored the substituent effect on the oxidative addition step, the known rate determining step of the whole reaction, by density functional theory (DFT) calculation. The key aryl ring on the ligand skeleton, namely Ring A, acts as a π-donor and stabilizes the palladium center of the transition state, as shown by Extended Transition State Natural Orbital of Chemical Valance (ETS-NOCV) analysis, and thus an electron-rich Ring A is expected to lower the barrier. On the other hand, however, the polarization and electrostatic effects were shown to be as or even more important, although they were often ignored before. These effects originate from through-space interaction with the nitro group in the resting state, and the overall effect is that any polarizable or partly negative group nearby the ortho- or meta¬- site of Ring A is harmful for the reaction. Based on these discoveries, we proposed a list of guidelines for successful ligand development, and designed several new ligands. These ligands exhibit significantly lower barrier than the reported Nakao’s ligand by as large as ~5 kcal/mol in both gas phase and solvation, and might be good candidates for further experimental study.
The role of language in students’ justifications of scientific phenomena
Authors: Deng Jacky , Rahmani Malek , Flynn Alison
Published: February 2022

Constructing scientific arguments is an essential skill for members of society, especially in a world facing complex socioscientific issues. Educators can help students develop scientific argumentation skills; however, argumentation is a complex linguistic practice and little is known about how English language learners construct arguments in English. We investigated how undergraduate science students’ English language proficiency and history were associated with their level of reasoning in scientific arguments (N = 166). We found that participants’ English language experiences, including their proficiency and history, were associated with the level of reasoning demonstrated. These findings suggest a need to identify the associated barriers faced by students from diverse language backgrounds and design equitable educational supports and assessments.
The role of language in students’ justifications of scientific phenomena
Authors: Deng Jacky , Rahmani Malek , Flynn Alison
Published: February 2022

Making decisions and constructing arguments with scientific evidence and reasoning are essential skills for all members of society, especially in a world facing complex socioscientific issues (climate change, global pandemics, etc.). Argumentation is a complex linguistic practice, but little is known about how students from diverse language backgrounds engage in argumentation. The goal of this study was to identify how students’ English language proficiency/history was associated with the reasoning demonstrated in their written arguments. We found that students with lower English proficiency and less English history produced fewer causal responses compared to students with higher English language proficiency and history. Follow-up interviews with fifteen participants revealed that students’ comfort communicating in English on assessments depended on a combination of general and academic language experiences. Findings suggest a need to identify what barriers students from diverse language backgrounds encounter during argumentation to ensure students from all language backgrounds have equitable opportunities to demonstrate their abilities.
Integration of biowaste into chemical reaction networks
Authors: Arun Adarsh , Weber Jana , Guo Zhen , Lapkin Alexei
Published: February 2022

As the chemical sector looks to decarbonize, one promising solution is the utilization of bio-feedstocks and biowaste to produce functional molecules. There is, therefore, great interest in understanding how and where to integrate these resources within chemical supply chains. To assist such efforts, screening methodologies relying on large reaction networks have recently been proposed.1,2 However, they are currently hindered by a lack of data for region-specific heterogenous raw materials compositions, as well as upstream pretreatments to isolate the important feedstocks. This study illustrates the workflow and data requirements of early stage biowaste stream evaluation through a case study on the waste landscape in and around the Singapore region. We first investigate biowaste sources that are available, stable in quantities, underutilized, pure, and yielding the feedstocks of interest. Oil palm empty fruit bunch (EFB), a lignocellulosic biowaste stream widely available in Malaysia and Indonesia, meets these criteria. We then simulate an ethanol organosolv pretreatment process for the fractionation of cellulose, lignin and xylose from EFB, and characterise the economic and environmental performances of the process through its exergy profile; this enables a link to chemical pathway identification in reaction networks. This study outlines the initial steps towards generating open datasets on biowaste for development of sustainable supply chains.
Determination of the Geographical Origin of Hazelnuts (Corylus avellana L.) by Near-Infrared Spectroscopy (NIR) and a Low-Level Fusion with Nuclear Magnetic Resonance (NMR)
Authors: Shakiba Navid , Gerdes Annika , Holz Nathalie , Wenck Sören , Bachmann René , Schneider Tobias , Seifert Stephan , Fischer Markus , Hackl Thomas
Published: February 2022

Fourier-transform near-infrared (FT-NIR) spectroscopy was used to determine the geographical origin of 233 hazelnut samples of various varieties from five different countries (Germany, France, Georgia, Italy, Turkey). The experimental determination of the geographical origin of hazelnuts is important, because there are usually large price differences between the producer countries and thus a risk of food fraud that should not be underestimated. The present work is a feasibility study using a low-cost method, as high-field NMR and UPLC-QTOF-MS have already been used for this question. Sample sets were split with repeated nested cross validation and an ensemble of discriminant classifiers with random subspaces was used to build the classification models. By using a preprocessing strategy consisting of multiplicative scatter correction, bucketing and the mean averaging of five measured spectra per sample, a test accuracy of 90.6 ± 3.9% was achieved, which rivals results obtained with much more expensive infrastructure. The application of the feature selection approach surrogate minimal depth showed that the successful classification is mainly caused by protein signals. In addition, a low-level data fusion of the NIR and NMR data was performed to assess how well the two methods complement each other. The data fusion was compared to a complementary approach, where the classification results based on the individual NIR and NMR models were jointly examined. The data fusion performed better than the individual methods with a test accuracy of 96.6 ± 2.8%. A comparison of the outliers in all classification models shows conspicuities in always the same samples, indicating that robust classification models are obtained.
Artificial stabilization of the fusion pore by intra-organelle styrene-maleic acid copolymers
Authors: Caparotta Marcelo , Puiatti Marcelo , Masone Diego
Published: February 2022

Styrene-maleic acid copolymers have become an advantageous detergent-free alternative for membrane protein isolation. Since their discovery, experimental membrane protein extraction and purification by keeping intact their lipid environment has become significantly easier. With the aim of identifying new applications of these interesting copolymers, their molecular binding and functioning mechanisms have recently been intense objects of study. In this work, we describe the use of styrene-maleic acid copolymers as an artificial tool to stabilize the fusion pore. We show that when these copolymers circumscribe the water channel that defines the fusion pore, they keep it from shrinking and closing. We describe how only intra-organelle copolymers have stabilizing capabilities while extra-organelle ones have negligible or even contrary effects on the fusion pore life-time.
Ebola: Destroys Na+/K+ Ion Exchange to Accelerate Electrolyte Imbalance by Scorpion Venom-like System
Authors: liu wenzhong , li hualan
Published: February 2022

Ebola sickness is a hemorrhagic fever caused by the Ebola virus that has an extremely high fatality rate. Electrolyte imbalance is a typical sign in Ebola patients who have already contracted the virus. The use of bioinformatics calculation tools to research Ebola's electrolyte imbalance mechanism is critical for halting the development of the epidemic and saving lives. The computational method of conserved domain search was employed to investigate the protein function of EBOV in this work. This study demonstrates that L, N, S, VP24, and VP35 have LCN type CS-α/β domains. It is a peptide neurotoxin found in scorpions, sea anemone, and snake venom. It can activate Na+ channels and gradually deactivate them, and deactivate voltage- and Ca+2-activated K+ channels. S LCN type CS-α/β is a neurotoxin with a lengthy chain that can activate Na+ channels. VP24, VP35, and N LCN type CS-α/β are short-chain toxins that inhibit voltage-dependent or Ca+2-activated K+ channels and partially inactivate sodium channels. L contains both long- and short-chain LCN type CS-α/β toxins that can activate Na+ channels and inhibit K+ channels. These LCN type CS-α/β can activate Na+ channels and Na+/K+ pumps while simultaneously inactivating K+ channels. It may result in many Na+ entering the cell and a large amount of K+ accumulating within the cell. Simultaneously, the Na+/Ca+ exchange pump outputs Na+ and inputs Ca+2 in “the reverse” mode. The results in an electrolytic environment outside the cell with hyponatremia, hypocalcemia and hypokalemia.
A mechanism of abiogenesis based on complex reaction networks organized by seed-dependent autocatalytic systems
Authors: Peng Zhen , Linderoth Jeff , Baum David
Published: February 2022

The complexity gap between the biotic and abiotic worlds has made explaining abiogenesis one of the hardest scientific questions. A promising strategy for addressing this problem is to identify features shared by abiotic and biotic chemical systems that permit the stepwise accretion of complexity. Therefore, we compared abiotic and biotic reaction networks in order to evaluate the presence of autocatalysis, the underlying basis of biological self-propagation, and to see if the organization of autocatalytic motifs permits stepwise complexification. We provide an algorithm to detect seed-dependent autocatalytic systems (SDASs), namely subnetworks that can use food chemicals to self-propagate but must be seeded by some non-food chemicals to become activated. We show that serial activation of SDASs can cause incremental complexification. Furthermore, we identify life-like features that emerge during the accretion of SDASs, including the emergence of new ecological opportunities and improvements in the efficiency of food utilization. The SDAS concept explains how driven abiotic environments, namely ones receiving an ongoing flux of food chemicals, can incrementally complexify without the need for genetic polymers. This framework also suggests experiments that have the potential to detect the spontaneous emergence of life-like features, such as self-propagation and adaptability, in driven chemical systems.
Rational design of Two-dimensional Binary Polymers from Hetero Triangulenes for Photocatalytic Water Splitting
Authors: Zhou Zhenpei , Springer Maximilian , Geng Weixiang , Zhu Xinyue , Li Tianchun , Li Manman , Jing Yu , Heine Thomas
Published: February 2022

Based on first principles calculations, we report the design of three two-dimensional (2D) binary honeycomb-kagome polymers composed of B- and N-centered heterotriangulenes with a periodically alternate arrangement as in hexagonal boron nitride. The 2D binary polymers with donor-acceptor characteristics, are semiconductors with a direct band gap of 1.98-2.28 eV. The enhanced in-plane electron conjugation contributes to high charge carrier mobilities for both electrons and holes, about 6.70 and 0.24 × 103 cm2 V-1 s-1, respectively, for the 2D binary polymer with carbonyl bridges (2D CTPAB). With appropriate band edge alignment to match the water redox potentials and pronounced light adsorption for the ultraviolet and visible range of spectra, 2D CTPAB is predicted to be an effective photocatalyst/photoelectrocatalyst to promote overall water splitting.
Generalizable Features of Interfacial Water Structure Predict the Hydrophobicity of Chemically Heterogeneous Surfaces
Authors: Dallin Bradley , Kelkar Atharva , Van Lehn Reid
Published: February 2022

The hydrophobicity of an interface determines the magnitude of hydrophobic interactions that drive numerous biological and industrial processes. Chemically heterogeneous interfaces are abundant in these contexts; examples include the surfaces of proteins, functionalized nanomaterials, and polymeric materials. While the hydrophobicity of nonpolar solutes can be predicted and related to the structure of interfacial water molecules, predicting the hydrophobicity of chemically heterogeneous interfaces remains a challenge because of the complex, non-additive contributions to hydrophobicity that depend on the chemical identity and nanoscale spatial arrangements of polar and nonpolar groups. In this work, we utilize atomistic molecular dynamics simulations in conjunction with enhanced sampling and data-centric analysis techniques to quantitatively relate changes in interfacial water structure to the hydration free energies (a thermodynamically well-defined descriptor of hydrophobicity) of chemically heterogeneous interfaces. We analyze a large data set of 58 self-assembled monolayers (SAMs) containing ligands with nonpolar and polar end groups of different chemical identity (amine, amide, and hydroxyl) in five mole fractions, two spatial patterns, and with scaled partial charges. We find that only five features of interfacial water structure are required to accurately predict hydration free energies. Examination of these features reveals mechanistic insights into the interfacial hydrogen bonding behaviors that distinguish different surface compositions and patterns. This analysis also identifies the probability of highly coordinated water structures as a unique signature of hydrophobicity. These insights provide a physical basis to understand the hydrophobicity of chemically heterogeneous interfaces and connect hydrophobicity to experimentally accessible perturbations of interfacial water structure.
[FeFe] Hydrogenase based Prototype Photosensitizer-Catalyst Dyad for Hydrogen Generation under Visible Light
Authors: Buday Philipp , Kasahara Chizuru , Hofmeister Elisabeth , Kowalczyk Daniel , Farh Michael K. , Riediger Saskia , Schulz Martin , Wächtler Maria , Furukawa Shunsuke , Saito Masaichi , Ziegenbalg Dirk , Gräfe Stefanie , Bäuerle Peter , Kupfer Stephan , Dietzek-Ivanšić Benjamin , Weigand Wolfgang
Published: February 2022

Inspired by the active center of the natural [FeFe] hydrogenases, we designed a compact and precious metal-free photosensitizer-catalyst dyad (PS-CAT) for photocatalytic hydrogen evolution under visible light irradiation. PS-CAT represents a prototype dyad comprising pi-conjugated oligothiophenes as light absorbers. PS-CAT and its interaction with the sacrificial donor 1,3-dimethyl-2-phenylbenzimidazoline were studied by steady-state and time-resolved spectroscopy coupled with electrochemical techniques and visible light-driven photocatalytic investigations. Operando EPR spectroscopy revealed the formation of an active [Fe(I)Fe(0)] species – in accordance with theoretical calculations – presumably driving photocatalysis effectively (TON ≈ 210).
The Role of (tBuPOCOP)Ir(I) and iridium(III) Pincer Complexes in the Catalytic Hydrogenolysis of Silyl Triflates into Hydrosilanes
Authors: Durin Gabriel , Berthet Jean-Claude , Nicolas Emmanuel , Thuéry Pierre , Cantat Thibault
Published: February 2022

Hydrosilanes are convenient reductants for a large variety of organic substrates, but they are produced via energy-intensive processes. These limitations call for the development of general catalytic processes able to transform Si‒O into Si‒H bonds. We report here the catalytic hydrogenolysis of R3SiOTf (R = Me, Et, Ph) species in the presence of a base (e.g. NEt3), by the hydride complexes [(tBuPOCOP)IrH(X)] (X = H, OTf; (tBuPOCOP = [(1,3-C6H3)(OPtBu)2]). Syntheses and crystal structures of new iridium(I) and iridium(III) complexes are presented as well as their role in the R3SiOTf to R3SiH transformation. The mechanisms of these reactions have been examined by DFT studies, revealing that the rate-determining step is the base-assisted splitting of H2
Thermodynamic Modeling of CO2 Separation Systems with Soluble, Redox-Active Capture Species
Authors: Clarke Lauren E. , Leonard McLain E. , Hatton T. Alan , Brushett Fikile R.
Published: February 2022

Electrochemical approaches hold promise for energy-efficient and modular carbon dioxide (CO2) separation systems that can make direct use of renewably-generated electricity. Here we employ a thermodynamic modeling approach to estimate the upper performance bounds of CO2 separation processes that use soluble, redox-active capture species. We contemplate the impact of tunable molecular and electrolyte properties on the thermodynamic and faradaic efficiencies of four characteristic system configurations. We find a tradeoff between these efficiency metrics, and propose a new metric, the combined efficiency, that can be used to further explore this tradeoff and identify desirable property sets that balance energy and materials requirements. Subsequently, we determine effective CO2 binding affinities of redox-active capture molecules and demonstrate how these values are dependent upon molecular properties, system format, and operating conditions. Overall, this analytical framework can help guide molecular discovery and electrolyte engineering in this emerging field by providing insight into target material properties.
Modular Enantioselective Synthesis of cis-Cyclopropanes through Redox-Active Carbene Transfer and Stereoselective Photo-Decarboxylation
Authors: Costantini Matteo , Mendoza Abraham
Published: February 2022

Chiral cis-cyclopropanes are strained rigid analogs of alkyl chains, whose study and application is still limited by their difficult synthesis. A modular approach for the synthesis of this challenging structures from abundant olefins is enabled by the discovery of the electron donor-acceptor (EDA) interaction between 2-substituted benzothiazolines and N-hydroxyphtalimide esters. These complexes are activated by visible light without photocatalysts. In this system, the benzothiazoline reagent plays a triple role as photoreductant, stereoselective hydrogen atom donor and Brønsted acid. Beyond the enantioselective synthesis of cis-cyclopropanes, these results introduce benzothiazolines as accessible and easily tunable self-sensitized photoreductants.
Electrochromism or Water Splitting in Neutral Aqueous Solutions by a Metallo-Organic Assembly
Authors: Malik Naveen , Bendikov Tatyana , Lahav Michal , van der Boom Milko
Published: February 2022

We describe two different functionalities of one metallo-organic film assembled on the surface of a transparent metal-oxide electrode. Two redox-active elements, electrochromic iron-polypyridyl complexes and catalytically-active palladium centers, operate by applying different potentials in aqueous solutions. The color of the material can be cycled 1500 times from dark purple to colorless by electrochemically addressing the Fe2+/3+ centers at 0.0-1.0 V (vs Ag/Ag+). The differences between the transmittance of these two states is high: ΔT = 52%. Catalytic water oxidation can occur by palladium oxide particles that form in-situ by applying a higher potential (1.22-2.0 V vs Ag/Ag+), resulting in the formation of dihydrogen and oxygen. The product output is stable for at least 7 hours in an aqueous electrolyte at pH = 6.9, with a Faradaic efficiency (FE) of ~70%.
Probing the Edges between Stability and Degradation of a Series of ZnSe-Based Layered Hybrid Semiconductors
Authors: Yan Mengwen , Feldblyum Jeremy , Chen Alan , Myers Christopher , John Gregory , Meyers Vincent
Published: February 2022

The discovery of layered materials with potentially unique electrical and chemical properties has become a major focus of materials research in the past decade. II-VI layered hybrids (LHs) are a family of ligand-protected layered materials capable of isolation in few-layer form and possess emissive and electronic properties of potential relevance to semiconductor device technologies. We showed previously that, akin to black phosphorus (BP) and transition metal dichalcogenides (TMDCs), II-VI LHs are sensitive to ambient atmospheric conditions. However, the causes for degradation of these ligand-protected materials remain unclear. Using ZnSe-based LHs, we show herein that the stability of these materials is related to the length and chemistry of the organic ligands coordinated to the LH surfaces. Furthermore, exposure to isotopically enriched H218O and 18O2 reveals that H2O and O2 are both reactants contributing to ZnSe-LH degradation. An H2O-initiated degradation pathway is proposed and is supported by density functional theory (DFT) calculations. Our findings contribute to the discovery of protection strategies for layered materials and elucidate a degradation pathway that may also be applicable to other layered materials.
Bromate incorporation in calcite and aragonite
Authors: Midgley Scott , Fleitmann Dominik , Grau-Crespo Ricardo
Published: February 2022

The presence of bromine as a trace-element in calcium carbonate speleothems constitutes a useful proxy of past volcanic activity, thus helping to provide input parameters for climate model simulations and risk assessment. However, the chemical nature of bromine-containing impurities in the calcium carbonate phases forming speleothems is not understood, which limits interpretation of experimental measurements on speleothems. We present here a computer simulation study, based on quantum mechanical calculations, of the incorporation of bromine as BrO3- oxyanions in CaCO3 polymorphs calcite and aragonite. We discuss how the relative distribution of bromate anions and charge-compensating alkali-metal cations is determined by the interplay between an impurity binding effect (which is stronger for aragonite than for calcite, and changes in the order Li
Accelerated Discovery of CH4 Uptake Capacity MOFs using Bayesian Optimization
Authors: Taw Eric , Neaton Jeffrey
Published: February 2022

High-throughput computational studies for discovery of metal-organic frameworks (MOFs) for separations and storage applications are often limited by the costs of computing thermodynamic quantities, with recent studies reliant ab initio results for a narrow selection of MOFs and empirical force-field methods for larger selections. Here, we conduct a proof-of-concept study using Bayesian optimization on CH4 uptake capacity of hypothetical MOFs for an existing dataset (Wilmer et al, Nature Chem. 2012, 4, 83). We show that less than 0.1% of the database needs to be screened with our Bayesian optimization approach to recover the top candidate MOFs. This opens the possibility of efficient screening of MOF databases using accurate ab-initio calculations for future adsorption studies on a minimal subset of MOFs. Furthermore, Bayesian optimization and the surrogate model presented here can offer interpretable material design insights and our framework will be applicable in the context of other target properties.
Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally-controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells using Long Wavelength Light
Authors: Jemas Andrew , Xie Yixin , Pigga Jessica , Caplan Jeffrey , am Ende Christopher , Fox Joseph
Published: February 2022

Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as “CABL”. Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dieno-phile. 6-(2-Pyridyl)-dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation pro-duce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 106 M-1s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore was demonstrated. CABL is light-dose dependent, and 2-photon excitation promotes CABL at the sub-organelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous pro-tein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small mole-cule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of ‘ordinary’ tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.
Leaflet Asymmetry Modeling in Lipid Composition of Escherichia coli Cytoplasmic Membrane
Authors: Hsieh Min-Kang , Klauda Jeffery
Published: February 2022

Lipid composition asymmetry between leaflets is important to cell function and plays a key role in the “positive inside” rule in transmembrane proteins. In this work, E. coli inner plasma membrane models reflecting this asymmetry have been investigated at the early-log and stationary stages during the bacterial lifecycle using all-atom molecular dynamics simulations. The CHARMM36 lipid force field is used, and selected membrane properties are tested for variations between two leaflets and whole membranes. Our models include bacterial lipids containing cyclopropane moiety on the sn-2 acyl chain in the stationary membrane. The PE:PG ratio in two leaflets reflects the “positive inside” rule of membrane proteins, set to 6.8 and 2.8 for the inner and outer leaflets of the two models. We are the first to model leaflet asymmetry in lipid composition on E. Coli cytoplasmic membrane and observe the effect on membrane properties in leaflets and whole membranes. Specifically, our results show that for the stationary phase bilayer, the surface area per lipid (SA/lipid) is larger, the thickness (2DC and DB) is thinner, the tilt angle is larger, the tilt modulus is smaller, and the deuterium order parameter (SCD) of sn-1 and sn-2 tails are lower, compared to the early-log stage. Moreover, the stationary stage bilayer has a negative spontaneous curvature while the early-log stage is near flat spontaneous curvature. For leaflet asymmetry, the inner leaflet has a larger SA/lipid, a smaller thickness, a smaller elastic tilt modulus (a larger tilt angle), and low SCD, compared to the outer leaflet in both stages. Moreover, asymmetric membrane involves a lipid tilt and a lateral extension, varying from a reference state of pre-equilibrium membrane. This work encourages a more profound exploration of leaflet asymmetry in various other membrane models and specifically how this might affect structure and function of membrane-associated peptides and proteins.
Highly efficient and stable Ru nanoparticle electrocatalyst for the hydrogen evolution reaction in alkaline conditions
Authors: Søndergaard-Pedersen Frederik , Lakhotiya Harish , Bondesgaard Martin , Myekhlai Munkhshur , Benedetti Tania M. , Gooding J. Justin , Tilley Richard D. , Iversen Bo B.
Published: February 2022

Developing alternatives to platinum-based electrocatalysts for the hydrogen evolution reaction (HER) is an important challenge for realizing the green transition. This is especially the case for alkaline conditions where Pt-based catalysts have very poor stability. Here, we demonstrate new solvothermal synthesis methods with facile allotropism control for selectively obtaining hexagonal-close-packed (hcp) and face-centered cubic (fcc) ruthenium nanoparticles. Both samples are highly active HER catalysts in alkaline conditions outperforming commercial Pt/C. However, the samples show markedly different stabilities. The hcp sample shows exceptional stability for 12 hours constant operation at 10 mA/cm2 with an overpotential that only increases 6 mV whereas the fcc sample increases 50 mV and the commercial Pt/C more than 350 mV. Thus, this study underlines the importance of controlling the crystal structure of nanoparticle electrocatalysts and shows the potential of using Ru as an alternative to Pt in alkaline conditions.
A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy
Authors: Jiménez-Grávalos Fernando , Suárez Dimas
Published: February 2022

Basing on the interacting quantum atoms approach, we present a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the non-covalent complexes in the S66 database, the fragment and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.
Modulating the Conductance in Graphene Nanoribbons with Multi-Barriers Under an Applied Voltage
Authors: Dakhlaoui Hassen , Almansour Shaffa , Belhadj Walid , Wong Bryan
Published: February 2022

The electronic transmission and conductance produced by Dirac electrons in an armchair graphene nanoribbon under an external voltage are investigated with the transfer matrix method. We investigate the velocity and voltage of nanoribbons in the presence of single and multiple barriers and show that the transmission coefficients can be controlled by varying the order of the mode, the number of carbon atoms, and the barrier velocities. In particular, we find that the nanoribbon appears to be fully transparent when the barrier and Fermi velocities are equal. Our numerical results show that the electronic conductance is sensitive to the applied external voltage and number of carbon atoms, which can be used to tailor the electronic properties of graphene-based devices.
Aza-SAHA Derivatives are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation
Authors: Steimbach Raphael R. , Herbst-Gervasoni Corey J. , Klinke Glynis , Géraldy Magalie , Tihanyi Gergely , Ridinger Johannes , Poschet Gernot , Oehme Ina , Christianson David W. , Gunkel Nikolas , Miller Aubry K.
Published: February 2022

We report the first selective chemical probes for histone deacetylase 10 (HDAC10) with unprecedented selectivity over other HDAC isozymes. HDAC10 deacetylates polyamines and has a distinct substrate specificity, making it unique among the 11 zinc-dependent HDAC hydrolases. Taking inspiration from HDAC10 polyamine substrates, we systematically inserted an amino group (“aza-scan”) into the hexyl linker moiety of the approved drug Vorinostat (SAHA). This one atom replacement (C-->N) transformed SAHA from an unselective pan-HDAC inhibitor into a specific HDAC10 inhibitor. Optimization of the aza-SAHA structure yielded DKFZ-748, which has a double-digit nanomolar IC50 against HDAC10 in cells and >500-fold selectivity over the closest relative HDAC6 as well as the Class I enzymes (HDAC1, 2, 3, 8). Potency of our aza-SAHA derivatives is rationalized with HDAC10 co-crystal structures and demonstrated by cellular and biochemical target-engagement, as well as thermal-shift, assays. Treatment of cells with DKFZ-748, followed by quantification of selected polyamines, confirmed for the first time the suspected cellular function of HDAC10 as a poly-amine deacetylase. Selective HDAC10 chemical probes provide a valuable pharmacological tool for target validation and will enable further studies on the enigmatic biology of HDAC10 and acetylated polyamines. HDAC10-selective aza-SAHA derivatives are not cytotoxic, which opens the doors to novel therapeutic applications as immunomodulators or in combination cancer therapy.
Automated handling of complex chemical structures in Z-matrix coordinates - the chemcoord library
Authors: Weser Oskar , Hanke Björn Hein , Mata Ricardo
Published: February 2022

In this work, we present a fully automated method for the construction of chemically meaningful sets of non-redundant internal coordinates (also commonly denoted as Z-matrices) from the cartesian coordinates of a molecular system. Particular focus is placed on avoiding ill-definitions of angles and dihedrals due to linear arrangements of atoms, to consistently guarantee a well-defined transformation to cartesian coordinates, even after structural changes. The representations thus obtained are particularly well suited for pathway construction in double-ended methods for transition state search and optimisations with non-linear constraints. Analytical gradients for the transformation between the coordinate systems were derived for the first time, which allows analytical geometry optimizations purely in Z-matrix coordinates. The geometry optimisation was coupled with a Symbolic Algebra package to support arbitrary non-linear constraints in Z-matrix coordinates, while retaining analytical energy gradient conversion. Sample applications are provided for a number of common chemical reactions and illustrative examples where these new algorithms can be used to automatically produce chemically reasonable structure interpolations, or to perform non-linearly constrained optimisations of molecules.
A Reproducible and Scalable Method for Producing Fluorescent Polystyrene Nanoparticles
Authors: Bartoš Dávid , Wang Lu , Anker Andy S. , Rewers Morten , Aalling-Frederiksen Olivia , Jensen Kirsten Marie Ørnsbjerg , Sørensen Thomas Just
Published: February 2022

In this work polystyrene nanoparticles (PS NPs) were fabricated from an emulsion of PS/toluene in water using various surfactants, and purified via dialysis in a simple procedure. The synthesis process was carried out at room temperature, without hazardous chemicals, and with a workload of 5 hours. The investigation was performed to evaluate the limits for production of PS NPs with comparable properties. A robust PS NP synthesis procedure was developed, repeated, and tested by three independent researches. The procedure was up-scaled to prove the applicability of the method and the NPs were prepared with four different hydrophobic dyes. All products were found to be comparable, and it was concluded that the method reported here can provide PS NPs with or without dye dopants, and that it provides access to PS NPs with an average diameter of 25 nm in a reproducible size distribution.