bluuebunny/crossref_metadata_2025 huggingface dataset:
High precision evaluation of the combustion enthalpy by ab-intio computations
Authors: Alibakhshi Amin
Published: February 2022

Accurate evaluation of combustion enthalpy is of high scientific and industrial importance. Although via ab-initio computation of heat of reactions, as one of the promising and well-established approaches in computational chemistry, this goal should in principle be achievable, examples of reliable and precise evaluation of heat of combustion by ab-initio methods has surprisingly not yet been reported. A handful of works carried out for this purpose report significant inconsistencies between the ab-initio evaluated and experimentally determined combustion enthalpies and suggest empirical corrections to improve the accuracy of predicted data. With this background, the main aims of the present study is to investigate the reasons behind those reported inconsistencies and propose guidelines for highly accurate evaluation of combustion enthalpy via ab-initio computations. Through the provided guidelines, the most accurate results ever reported, with average absolute deviation, mean unsigned error and correlation coefficient of 1.556 kJ/mole, 0.072% and 0.99999, respectively, is achieved for theoretically computed combustion enthalpies of 40 studied hydrocarbons.
Small but effective: light-weight additives modulate prenucleation clusters by specific interactions on the molecular level
Authors: Duchstein Patrick , Schodder Philipp I. , Leupold Simon , Dao Thi Quynh Nhi , Kababya Shifi , Schmidt Asher , Cicconi Maria R. , de Ligny Dominique , Pipich Vitaliy , Eike David , Zahn Dirk , Wolf Stephan E.
Published: February 2022

Small-molecular-weight (MW) additives can strongly impact amorphous calcium carbonate (ACC), playing an elusive role in biogenic, geologic, and industrial calcification. Here, we present molecular mechanisms by which additives regulate stability and composition of solid ACC and CaCO3 solutions simultaneously. Effective precipitation inhibition arises from pronounced interaction of additives with prenucleation clusters (PNC). Potent antiscalants specifically trigger and integrate into PNCs. Only PNC-interacting additives are traceable in solid ACC, considerably stabilizing ACC against transformation. This co-precipitation specificity facilitates a chemical labeling of PNCs, evidencing ACC as a molecular precipitate of PNCs. Our results reveal additive-cluster interactions that operate beyond established mechanistic conceptions and thus reassess the role of small-MW molecules in crystallization and especially in biomineralization while breaking grounds for new sustainable antiscalants.
Reproducible Untargeted Metabolomics Data Analysis Workflow for Exhaustive MS/MS Annotation
Authors: Yu Miao , Dolios Georgia , Petrick Lauren
Published: February 2022

Motivation Unknown features in untargeted metabolomics and non-targeted analysis (NTA) are identified using fragment ions from MS/MS spectra to predict the structures of the unknown compounds. The precursor ion selected for fragmentation is commonly performed using data dependent acquisition (DDA) strategies or following statistical analysis using targeted MS/MS approaches. However, the selected precursor ions from DDA only cover a biased subset of the peaks or features found in full scan data. In addition, different statistical analysis can select different precursor ions for MS/MS analysis, which make the post-hoc validation of ions selected by new statistical methods impossible for precursor ions selected by the original statistical method. By removing redundant peaks and performing pseudo-targeted MS/MS analysis on independent peaks, we can comprehensively cover unknown compounds found in full scan analysis using a “one peak for one compound” workflow without a priori redundant peak information. Here we propose an reproducible, automated, exhaustive, statistical model-free workflow: paired mass distance-dependent analysis (PMDDA), for untargeted mass spectrometry identification of unknown compounds found in MS1 full scan. Results More annotated compounds/molecular networks/spectrum were found using PMDDA compared with CAMERA and RAMClustR. Meanwhile, PMDDA can generate the preferred ions list for iterative DDA to cover more compounds when instruments support such functions. Availability and implementation The whole workflow is fully reproducible as a docker image xcmsrocker with both the original data and the data processing template. https://hub.docker.com/r/yufree/xcmsrocker A related R package is developed and released online: https://github.com/yufree/rmwf. R script, data files and links of GNPS annotation results including MS1 peaks list and MS2 MGF files were provided in supplementary information.
Atomistic Nodal Approach: a General Molecular Dynamics Method For Computing Local Thermal Conductance at Atomistic Resolution
Authors: Jiang Mingxuan , Olarte-Plata Juan D. , Bresme Fernando
Published: February 2022

The Interfacial Thermal Conductance (ITC) is a fundamental property of materials and has particular relevance at the nanoscale. The ITC quantifies the thermal resistance between materials of different compositions or between fluids in contact with materials. Furthermore, the ITC determines the rate of cooling/heating of the materials and the temperature drop across the interface. Here we propose a method to compute local ITCs and temperature drops of nanoparticle-fluid interfaces. Our approach resolves the ITC at the atomic level using the atomic coordinates of the nanomaterial as nodes to compute local thermal transport properties. We obtain high-resolution descriptions of the interfacial thermal transport by combining the atomistic nodal approach, computational geometry techniques and "computational farming'' using Non-Equilibrium Molecular Dynamics simulations. We illustrate our method by analyzing various nanoparticles as a function of their size and geometry, targeting experimentally relevant structures like capped octagonal rods, cuboctahedrons, decahedrons, rhombic dodecahedrons, cubes, icosahedrons, truncated octahedrons, octahedrons and spheres. We show that the ITC of these very different geometries can be accurately described in terms of the local coordination number of the atoms in the nanoparticle surface. Nanoparticle geometries with lower surface coordination numbers feature higher ITCs, and the ITC generally increases with decreasing particle size.
Fragment-based Sequential Translation for Molecular Optimization
Authors: Chen Benson , Fu Xiang , Jaakkola Tommi , Barzilay Regina
Published: February 2022

Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instead propose a flexible editing paradigm that generates molecules using learned molecular fragments---meaningful substructures of molecules. To do so, we train a variational autoencoder (VAE) to encode molecular fragments in a coherent latent space, which we then utilize as a vocabulary for editing molecules to explore the complex chemical property space. Equipped with the learned fragment vocabulary, we propose Fragment-based Sequential Translation (FaST), which learns a reinforcement learning (RL) policy to iteratively translate model-discovered molecules into increasingly novel molecules while satisfying desired properties. Empirical evaluation shows that FaST significantly improves over state-of-the-art methods on benchmark single/multi-objective molecular optimization tasks.
Multi-electron excitation contributions towards primary and satellite states in the photoelectron spectrum
Authors: Moitra Torsha , Paul Alexander C. , Decleva Piero , Koch Henrik , Coriani Sonia
Published: February 2022

The computation of Dyson orbitals and corresponding ionization energies has been implemented within the Equation of Motion Coupled Cluster Singles, Doubles, and Perturbative Triples (EOMCC3) method. Coupled to an accurate description of the electronic continuum via a time-dependent density functional approach using a multicentric B-spline basis, this yields highly accurate photoionization dynamical parameters (cross-sections, branching ratios, asymmetry parameters, and dichroic coefficients) for primary states (1h) as well as satellite states of (2h-1p) character. Illustrative results are presented for the molecular systems H2O, H2S, CS, CS2 and (S)-propylene oxide (a.k.a. methyloxirane).
In Silico Discovery of Multistep Chemistry Initiated by a Conical Intersection: The Challenging Case of Donor Acceptor Stenhouse Adducts
Authors: Sanchez David M. , Raucci Umberto , Martínez Todd J.
Published: February 2022

Detailed mechanistic understanding of multistep chemical reactions triggered by internal conversion via a conical intersection is a challenging task that emphasizes limitations in theoretical and experimental techniques. Hypothesis-driven methodologies (e.g. characterization of critical points and biased molecular dynamics) are commonly employed to explore chemical space and simulate reaction events. In this contribution, we present a discovery-based, hypothesis-free computational approach based on first principles molecular dynamics to discover and refine the switching mechanism of Donor-Acceptor Stenhouse Adducts (DASAs). Using state-of-the-art graphical processing units-enabled electronic structure calculations we performed in total ~2ns of adiabatic and non-adiabatic ab initio molecular dynamics discovering a) critical intermediates that are involved in the open-to-closed transformation, b) several competing pathways which lower the overall switching yield, and c) key elements for future design strategies. Our dynamics describe the natural evolution of both the nuclear and electronic degrees of freedom that govern the interconversion between DASA ground state intermediates exposing significant elements for the future design strategies of molecular switches.
Enzyvitands: versatile evolvable colorimetric chembioreceptors
Authors: Rossel Thibaud , Bing zhang , Gobat Raphael
Published: February 2022

Designing the perfect sensor is the dream of any chemist. Since decades, a wide diversity of synthetic receptors targeting analytes has been explored in chemistry. Their chemical optimization is hard and with no guarantee of success. In this context, we propose a fast and self assembling colorimetric bio-chemical receptor coined Enzyvitand. It consists only of commercial chemicals. It relies on the reunification of combinatorial chemistry, first and second coordination spheres interactions and indicators displacement assays. All harbored within a protein cavity. The sensor is highly modular, cheap and evolvable. Thanks to its solved X-ray structure, we rationally designed it for the selectiv naked-eye recognition of dopamine over other neutrotransmitters through second coordination sphere. Hence, our sensor imitates a biological receptor for the recognition of neurotransmitters. Finally, it works in complex samples such as urine. Its immediate high versatility and evolvability is valuable for the selective detection of a wide assortment of analytes from small molecules up to micro-organisms. For the future, we anticipate new biotechnological or immunotherapeutic applications of our synthetic oligomer.
PhotoPhage: A Virus-based Photothermal Therapeutic Agent
Authors: Shahrivarkevishahi Arezoo , Luzuriaga Michael A. , Herbert Fabian C. , Tumac Alisia C. , Brohlin Olivia R. , Wijesundara Yalini H. , Benjamin Candace , Lee Hamilton , Parsamian Perouza , Gassensmith Jeremiah J.
Published: February 2022

ABSTRACT: Virus-like particles (VLPs) are multifunctional nanocarriers with the pathogenic-like architecture of viruses. They can serve as a safe platform for specific functionalization and immunization, which provides benefits in a wide range of biomedical applications. In this work, a new generation immunophotothermal agent is developed that adjuvants the photothermal ablation using a chemically modified VLP called bacteriophage Qβ. The design is based on the conjugation of near-infrared absorbing croconium dyes to lysine residues located on the surface of Qβ, which turns it to a powerful NIR-absorber called PhotoPhage. This system can generate more heat upon 808 nm NIR laser radiation than free dye with a photothermal efficiency comparable to gold nanostructures yet is biodegradable and acts as an immunoadjuvant combined with the heat it produces. The synergistic combination of thermal ablation with the mild immunogenicity of the VLP leads to effective suppression of primary tumors, reduced lung metastasis, and increased survival time.
The surface tension and interfacial composition of water/ethanol mixture
Authors: Phan Chi
Published: February 2022

This study develops a model to fit the surface tension of the water/ethanol mixture for the complete composition range from 0 to 1. The theoretical framework complements Van Der Waals’s theory on the density gradient. The modelling results overcome the limitation of Gibbs adsorption isotherm, which completely ignores the composition of the interfacial layer. Furthermore, the model presents a new method to correctly calculate the composition of the interfacial layer for binary liquid mixture and surfactant solutions.
Hydrogen Bonding Networks Enable Brønsted Acid-Catalyzed Carbonyl-Olefin Metathesis
Authors: To Tuong Anh , Pei Chao , Koenigs Rene , Nguyen Thanh Vinh
Published: February 2022

Synthetic chemists have learned to mimic nature in using hydrogen bonds and other weak interactions to dictate the spatial arrangement of reaction substrates and to stabilize transition states to enable highly efficient and selective reactions. The activation of a catalyst molecule itself by hydrogen bonding networks, in order to enhance its catalytic activity to achieve a desired reaction outcome, is less explored in organic synthesis, despite being a commonly found phenomenon in nature. Herein, we show our investigation into this underexplored area by studying the promotion of carbonyl-olefin metathesis reactions by hydrogen bonding-assisted Brønsted acid catalysis, using hexafluoroisopropanol (HFIP) solvent in combination with para-toluenesulfonic acid (pTSA). Our experimental and computational mechanistic studies reveal not only an interesting role of HFIP solvent in assisting pTSA Brønsted acid catalyst, but also insightful knowledge about the current limitations of the carbonyl-olefin metathesis reaction.
Remote Learning of COVID-19 Kinetic Analysis in a Physical Chemistry Laboratory Class
Authors: Hart Kelle , Thompson Chelsea , Burger Clay , Hardwick Dylan , Michaud Amanda , Al Bulushi Abdul H.M. , Pridemore Cole , Ward Carson , Chen Jixin
Published: February 2022

The COVID-19 pandemic has affected many in-person laboratory courses across the world. The viral spreading model is complicated but parameters, such as its reproduction number, Rt, can be estimated with the susceptible, infectious, or recovered (SIR) model. COVID-19 data for many states and countries are widely available online. This provides an opportunity for the students to analyze its spreading kinetics remotely. Here, we reported a lab carried out online during the third week of the spring semester of 2021 to minimize social contacts. Due to the wide interest in developing online physical chemistry and analytical labs during the pandemic, we’d like to share this lab design. The method, technique, procedure, and grading are described in this report. The student participants were able to apply the kinetic techniques learned in physical chemistry to successfully analyze an ongoing real-world problem through a remote learning environment and prepare this report.
Validation of the triplet ground state in a persistent derivative of Clar’s hydrocarbon
Authors: Valenta Leoš , Mayländer Maximilian , Kappeler Pia , Blacque Olivier , Šolomek Tomáš , Richert Sabine , Juríček Michal
Published: February 2022

Triangulene is a prototypical non-Kekulé diradical known as Clar’s hydrocarbon. It is the smallest non-Kekulé graphene fragment comprised of six benzenoid rings fused in a triangular shape. In accordance with Hund’s rule, a triplet ground state is predicted for this hydrocarbon. However, because of its high reactivity, synthesis of a stable or persistent derivative of neutral triangulene to validate this prediction has been an elusive goal for almost 70 years. Herein, we report the synthesis and characterization of the first persistent derivative of triangulene, kinetically stabilized by three sterically demanding substituents installed at the most reactive positions in the centers of the zigzag edges. The triplet ground state of this hydrocarbon is unequivocally confirmed by pulse electron paramagnetic resonance spectroscopy and supported by density functional theory. The realization of a long-sought-after persistent triangulene derivative will motivate the synthesis of analogous open-shell graphene fragments as prospective building blocks of high-spin materials for the newly emerging field of organic spintronics.
AMPA GluA2 subunit competitive inhibitors for PICK1 PDZ domain: Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and ADME studies
Authors: Rathod Shravan B. , Prajapati Pravin B. , Pal Ranjan , Mansuri Mohmedyasin F.
Published: February 2022

PICK1 (Protein interacting with C kinase-1) plays a key role in the regulation of intracellular trafficking of AMPA GluA2 subunit that is linked with synaptic plasticity. PICK1 is a scaffolding protein and binds numerous proteins through its PDZ domain. Research showed that synaptic plasticity is altered upon disrupting the GluA2-PDZ interactions. Inhibiting PDZ and GluA2 binding lead to beneficial effects in the cure of neurological diseases thus, targeting PDZ domain is proposed as a novel therapeutic target in such diseases. For this, various classes of synthetic peptides were tested. Though small organic molecules have been utilized to prevent these interactions, the number of such molecules is inadequate. Hence, in this study, ten molecular libraries containing large number of molecules were screened against the PDZ domain using pharmacophore-based virtual screening to find the best hits for the PDZ domain. Molecular docking and molecular dynamics simulation studies revealed that Hit_II is a potent inhibitor for the PDZ domain and confirm the allosteric nature of Hit_III. Additionally, ADME analysis suggests the drug-likeness of both Hit_II and Hit_III. This study suggests that tested hits may have potency against the PDZ domain and can be considered effective to treat neurological disorders.
OLED from solution-processed crystalline poly(triazine imide)
Authors: Burmeister David , Tran Ha Anh , Müller Johannes , Guerrini Michele , Cocchi Caterina , Plaickner Julian , Bojdys Michael
Published: February 2022

Crystalline semiconducting carbon nitrides are chemically and physically resilient, consist of earth abundant elements, and can be exfoliated into 2D atomically thin layers. In particular, poly(triazine imide) (PTI) is a highly crystalline semiconductor, and though no techniques exist to date that enable synthesis of macroscopic monolayers of PTI, it is possible to study it in thin layer device applications that are compatible with its polycrystalline, nanoscale morphology. In our study, we find that the by-product of conventional PTI synthesis is a C-C carbon rich phase that is detrimental for charge transport and photoluminescence. An optimised synthetic protocol yields a PTI material with an increased quantum yield, enabled photocurrent and electroluminescence. In addition, we report that protonation of the PTI structure happens preferentially at the pyridinic nitrogen atoms of the triazine (C3N3) rings, is accompanied by exfoliation of PTI layers, and contributes to increases in quantum yield and exciton lifetimes. This study describes structure-property relationships in PTI that link (i) the nature of defects, their formation, and how to avoid them with (ii) the optical and electronic performance of PTI. On the basis of our findings, we create an OLED prototype with PTI as the active, metal-free material, and we lay the foundations for device integration of solution-processable graphitic carbon nitride dispersions in semiconductor devices.
Performance comparison of r2SCAN and SCAN metaGGA density functionals for solid materials via an automated, high-throughput computational workflow
Authors: Kingsbury Ryan , Gupta Ayush , Bartel Christopher , Munro Jason , Dwaraknath Shyam , Horton Matthew , Persson Kristin
Published: February 2022

Computational materials discovery efforts utilize hundreds or thousands of density functional theory (DFT) calculations to predict material properties. Historically, such efforts have performed calculations at the generalized gradient approximation (GGA) level of theory due to its efficient compromise between accuracy and computational reliability. However, high-throughput calculations at the higher metaGGA level of theory are becoming feasible. The Strongly Constrainted and Appropriately Normed (SCAN) metaGGA functional offers superior accuracy to GGA across much of chemical space, making it appealing as a general-purpose metaGGA functional, but it suffers from numerical instabilities that impede it's use in high-throughput workflows. The recently-developed r2SCAN metaGGA functional promises accuracy similar to SCAN in addition to more robust numerical performance. However, its performance compared to SCAN has yet to be evaluated over a large group of solid materials. In this work, we compared r2SCAN and SCAN predictions for key properties of approximately 6,000 solid materials using a newly-developed high-throughput computational workflow. We find that r2SCAN predicts formation energies more accurately than SCAN and PBEsol for both strongly- and weakly-bound materials and that r2SCAN predicts systematically larger lattice constants than SCAN. We also find that r2SCAN requires modestly fewer computational resources than SCAN and offers much more reliable convergence. Thus, our large-scale benchmark confirms that r2SCAN has delivered on its promises of numerical efficiency and accuracy, making it an ideal choice for high-throughput metaGGA calculations.
Eukaryotic catecholamine hormones influence the chemotactic control of Vibrio campbellii by binding to the coupling protein CheW
Authors: Weigert Muñoz Angela , Hoyer Elisabeth , Schumacher Kilian , Grognot Marianne , Taute Katja , Hacker Stephan , Sieber Stephan , Jung Kirsten
Published: February 2022

In addition to their well-known role as stress-associated catecholamine hormones in animals and humans, epinephrine (EPI) and norepinephrine (NE) act as interkingdom signals between eukaryotic hosts and bacteria. However, the molecular basis of their effects on bacteria is not well understood. In initial phenotypic studies utilizing Vibrio campbellii as a model organism, we characterized the bipartite mode of action of catecholamines, which consists of promotion of growth under iron limitation, and enhanced colony expansion on soft agar. In order to identify the molecular targets of the hormones, we designed and synthesized tailored probes for chemical proteomic studies. As the catechol group in EPI and NE acts as iron chelator and is prone to form a reactive quinone moiety, we devised a photoprobe based on the adrenergic agonist phenylephrine (PE), which solely influenced colony expansion. Using this probe, we identified CheW, located at the core of the chemotaxis signaling network, as a major target. In vitro studies confirmed that EPI, NE, PE, as well as labetalol, a clinically applied antagonist, bind to purified CheW with affinity constants in the sub-micromolar range. In line with these findings, exposure of V. campbellii to these adrenergic agonists affects the chemotactic control of the bacterium. This study highlights a previously unknown effect of eukaryotic signaling molecules on bacterial motility.
Preparation of Recyclable and Versatile Porous Poly-Arylthioethers by Reversible Pd-Catalysed C–S/C–S Metathesis
Authors: Rivero-Crespo Miguel A. , Toupalas Georgios , Morandi Bill
Published: February 2022

Porous organic polymers have shown a number of promising properties; however, their application is usually hampered due to the lability of their linkages. Inspired by the outstanding chemical, mechanical and thermal resistance of the 1D polymer polyphenylene sulphide (PPS), we have designed a new family of 2D and 3D poly-arylthioethers, synthesised via a mild Pd-catalysed C–S/C–S metathesis-based method, that merges the attractive features common to porous polymers and PPS in a single material. In addition, the method is highly modular, allowing to easily introduce application-oriented functionalities in the materials for a series of environmentally relevant applications including metal capture, metal sensing and heterogeneous catalysis. Moreover, despite their extreme chemical resistance, the polymers can be easily recycled to recover the original monomers, offering an attractive perspective for their sustainable use.
The zwitterion isomer of orthosilicic acid and its role in neutral pH dimerization from density functional theory.
Authors: Felipe Mihali
Published: February 2022

Using density functional theory, the plausible existence of the zwitterion isomer of orthosilicic acid is proposed to account for some of the properties of silica in water. Explicit hydration and explicit addition of salt are used in modeling the zwitterion and the dimerization reaction. Paths between orthosilicic acid, the zwitterion and the autoionization products are presented. The pK for the formation of the aqueous zwitterion species is calculated to be 7.8 and the activation energy for the dimerization reaction ranges from 14.3 kcal/mol to 16.9 kcal/mol.
The yellow and the black of synthetic melanins
Authors: Vercruysse Koen , Govan Venise
Published: February 2022

The observations reported here are a continuation and expansion of observations described earlier: the typical conditions to synthesize melanin-like materials from catecholic precursors (air-oxidation in an alkaline environment) leads to the generation of a light-colored substance in addition to the typical dark substances. This light-colored substance appears to be associated with the dark-colored materials through non-covalent interactions. We employed a novel co-precipitation process that allows for a simple separation of this light-colored substance from the dark-colored materials. We studied some of the physic-chemical properties (color, fluorescence, FT-IR absorbance) of some of the fractions we obtained and discussed these properties in the context of what has been discussed for eumelanin, pheomelanin or neuromelanin. Overall, the current observations strengthen our hypothesis that synthetic melanins may be built from at least two types of substances: 1) a soluble, yellow-to-orange colored component, possibly rich in unoxidized precursors and 2) an insoluble, dark component. Our observations do suggest that when studying the chemistry or physiology of melanins one should look beyond the dark colors typically displayed by melanin-like materials.
Precise control of the degree and regioselectivity of functionalization in nitro- and amino-functionalized di(trispyrazolylborato)iron(II) spin crossover complexes
Authors: Ma Chenyang , Besson Claire
Published: February 2022

Di(trispyrazolylborato)iron(II) ([Tp2Fe]) complexes represent one of the most robust class of spin crossover complexes. Their stability renders them particularly suitable for integration in nanoscale devices, e.g. as sensors or information storage units. While prior studies of the functionalization of those derivatives have been focused on the electronic and steric effect of alkyl and -CF3 groups in position 3, a pyrazole exchange reaction between nitropyrazole and either trispyrazolylborate or its iron complex allows the regioselective installation of nitro substituents in positions 3, 4 and 5 of [Tp2Fe] complexes. The degree of substitution can be varied from 1 to 4 functionalized pyrazoles per complex. The amine functionalized analogues are accessed by reduction of the nitro analogues under hydrogen transfer conditions. With the exception of di- and tetra-3-NO2 substituted complexes, all derivatives display spin crossover properties in the solid state, with transition temperatures ranging from 180 to 380 K and showing different degree of abruptness, but no hysteresis. The Slichter-Drickamer model was used to extract empirical thermodynamic transition parameters, allowing a systematic investigation of the influence of stoichiometry, position, and electronic nature of the substitution on the magnetic properties of the complexes. Steric effects dominate for substitution in position 3, but electronic effects are significant for the other positions.
A General Method for Synthesis of Isomaleimide Derivatives
Authors: GONDI SUDERSHAN
Published: February 2022

A mild and efficient method for the synthesis of isoimide by a simple reaction of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) with various kinds of maleimicacid, succimicacid, pthaleimicacid in dichloromethane at room temperature is described.
Automated analysis of microplastics based on vibrational spectroscopy: Are we measuring the same metrics?
Authors: Dong Mingtan , She Zhenbing , Xiong Xiong , Luo Zejiao
Published: February 2022

The traditional manual analysis of microplastics has been criticized for its labor-intensive, inaccurate identification of very small microplastics (less than 10 µm), and the lack of uniformity between instrumentation techniques. There are already three automated analysis strategies for microplastics based on vibrational spectroscopy: laser direct infrared (LDIR)-based particle analysis, Raman-based particle analysis, and focal plane array-Fourier transform infrared (FPA-FTIR) imaging. We compared the performances of these strategies in terms of their quantification, detection limit, size measurement, and material identification accuracy and analysis speed by analyzing the same standard and environmental samples. Unfortunately, the automated analysis results are not consistent in terms of quantification and material identification. The number of particles smaller than 60 μm recognized by Raman-based particle analysis is far greater than that recognized by LDIR-based particle analysis. Raman-based particle analysis has a submicrometer detection limit but should not be used in the automated analysis of microplastics in environmental samples because of the strong fluorescence interference. LDIR-based particle analysis provides the fastest analysis speed, but we suggest using a reliable detection limit of approximately 60 μm and manually cross-check between the material identification results and the reference database used. Misidentification could occur due to the narrow tuning range from 1800 – 975 cm-1 and dispersive artefact distortion of infrared spectra collected in reflection mode. FPA-FTIR imaging provides relatively reliable quantification and material identification for microplastics in environmental samples greater than 20 µm but might provide an imprecise description of the particle shapes. Optical photothermal infrared (O-PTIR) spectroscopy can detect submicron-sized environmental microplastics (0.5-5 μm) intermingled with a substantial amount of biological matrix; the resulting spectra are searchable in infrared databases without the influence of fluorescence interference, but the process would need to be fully automated.
Effects of lateral-chain thiophene fluorination on morphology and charge transport of BDT-T based small molecule donors: A study with multiscale simulations
Authors: Xu Chunlin , Yao Chuang , Zheng Shaohui
Published: February 2022

Thiophene substituted benzo[1,2-b:4,5-b′]dithiophene (BDT-T) is widely used as the building block of promising donor materials in organic solar cells (OSCs). Fluorination on the lateral-chain thiophenes of BDT-T is a considerable strategy to further improve the performance of BDT-T based small molecule (SM) donors. However, how lateral-chain thiophene fluorination affects the morphology and hole mobility (μ_h) of SM donors has not been well understood. In the present work, we systematically study the effects of the positions and numbers of fluorinations on the morphology and μ_h of a promising SM donor named DRTB-T (referred as 0F) with multiple fluorinations via multiscale simulations. We find the crystallinity is weakened because of fluorination. The face-on configurations are dominated in 0F and 1F-substituted molecules. In contrast, the edge-on configurations are dominated in 2F-substituted molecules. The trend of μ_hs in these fluorinated molecules is consistent with that of the proportions of face-on configurations, and matches well with available experimental results. We find that functionalizing the lateral-chain thiophenes of side BDT-Ts (1F-side) or all BDT-Ts (1F-all) with only one F atom are efficient to fine-tune the morphologies and μ_h of DRTB-T based SM donors simultaneously.
Electronic structure and electron-transport properties of three metal hexacyanoferrates
Authors: Hurlbutt Kevin , Giustino Feliciano , Pasta Mauro , Volonakis George
Published: February 2022

Metal hexacyanometallates, or Prussian blue analogs (PBAs), are active materials in important electrochemical technologies, including next-generation sodium- and potassium- ion batteries. They have tunable properties including reduction potential, ionic conductivity, and color. However, little is known about their electronic conductivities. In this work, we use density-functional theory to model electronic structure and to explore the likely electron-conduction mechanism in three promising cathodes (manganese, iron, and cobalt hexacyanoferrate) in each of three oxidation states. First, we demonstrate that hybrid functionals reliably reproduce experimentally observed spin configurations and geometric phase changes. We confirm these materials are semiconductors or insu- lators with band gaps ranging from 1.90 eV up to 4.94 eV. We further identify that for most of the compounds the electronic band edges originate from carbon-coordinated- iron orbitals, suggesting that doping at the carbon-coordinated site may strongly affect carrier conductivity. Finally, we calculate charge-carrier effective masses, which we find are very heavy. This study is an important foundation for making electronic conductivity a tunable PBA material property.
On the climate impacts of blue hydrogen production
Authors: Bauer Christian , Treyer Karin , Antonini Cristina , Bergerson Joule , Gazzani Matteo , Gencer Emre , Gibbins Jon , Mazzotti Marco , McCoy Sean T. , McKenna Russell , Pietzker Robert , Ravikumar Arvind P. , Romano Matteo C. , Ueckerdt Falko , Vente Jaap , van der Spek Mijndert
Published: February 2022

Natural gas based hydrogen production with carbon capture and storage is referred to as blue hydrogen. If substantial amounts of CO2 from natural gas reforming are captured and permanently stored, such hydrogen could be a low-carbon energy carrier. However, recent research raises questions about the effective climate impacts of blue hydrogen from a life cycle perspective. Our analysis sheds light on the relevant issues and provides a balanced perspective on the impacts on climate change associated with blue hydrogen. We show that such impacts may indeed vary over large ranges and depend on only a few key parameters: the methane emission rate of the natural gas supply chain, the CO2 removal rate at the hydrogen production plant, and the global warming metric applied. State-of-the-art reforming with high CO2 capture rates combined with natural gas supply featuring low methane emissions does indeed allow for substantial reduction of greenhouse gas emissions compared to both conventional natural gas reforming and direct combustion of natural gas. Under such conditions, blue hydrogen is compatible with low-carbon economies and features climate change impacts in line with green hydrogen from electrolysis supplied with renewable electricity. However, neither current blue nor green hydrogen production pathways render fully “net-zero” hydrogen without additional carbon dioxide removal.
DeltaPCA: A Statistically Robust Method for Detecting Protein Analyte Binding to Aptamer-Functionalised Nanoparticles using Surface-Enhanced Raman Spectroscopy
Authors: Given Fiona , Stanborough Tamsyn , Waterland Mark , Crittenden Deborah
Published: February 2022

In this work, we introduce a novel joint experimental design and computational analysis procedure to reliably and reproducibly quantify protein analyte binding to DNA aptamer-functionalised silver nanoparticles using slippery surface-enhanced Raman spectroscopy. We employ an indirect detection approach, based upon monitoring spectral changes in the covalent bond-stretching region as intermolecular bonds are formed between the surface-immobilized probe biomolecule and its target analyte. Sample variability is minimized by preparing aptamer-only and aptamer-plus-analyte samples under the same conditions, and then analysing difference spectra. To account for technical variability, multiple spectra are recorded from the same sample. Our new DeltaPCA analysis procedure takes into account technical variability within each spectral data set while also extracting statistically robust difference spectra between data sets. Proof of principle experiments using thiolated aptamers to detect CoV-SARS-2 spike protein reveal that analyte binding is mediated through the formation of N-H...X and C-H...X hydrogen bonds between the aptamer (H-bond donor) and protein (H-bond acceptor). Our computational analysis code can be freely downloaded from https://github.com/dlc62/DeltaPCA.
Sustainability assessment of biodiesel produced from Jatropha curcas using life cycle assessment approach
Authors: Thakur Vijay , Chandel Munish
Published: February 2022

Transport sector in India is heavily dependent on fossil fuels and ~75% of the demand is met by import. National Biofuel Policy, 2009 focused on production of biodiesel from non-edible oil seeds. We assessed the sustainability of biodiesel produced from Jatropha curcas, using the life cycle assessment approach. India specific inventory data for biodiesel production was collected by extensive literature review. GaBi software was used to model the life cycle of biodiesel. The environmental impacts are compared for different blends of biodiesel with reference to diesel in four impact categories: Global Warming Potential, Acidification Potential, Eutrophication Potential, and Human Toxicity Potential. Using the biodiesel may reduce the global warming potential by 64.6% as compared to fossil diesel; while eutrophication potential, acidification potential, and human toxicity potential impacts may increase by 61.3%, 36.5%, and 52.5% respectively. A trade-off between impact categories is seen for biodiesel. Sensitivity analysis was done to identify most sensitive parameters in biodiesel life cycle. Use of electricity, life cycle span of Jatropha, seed yield, methanol, urea fertilizer, NOx emission factor, and steam are found to be highly sensitive in biodiesel life cycle. Scenario analysis was done to analyse the effect of change in seed yield, life span, and emission intensity of Indian electricity grid. Even low yield of Jatropha provides reduction in global warming potential (~27.7%) but in other impact categories significant increase is expected. Impacts could be further minimized if the emissions from grid are minimized in future.
Overcoming the Challenges towards Selective C(6)-H Alkylation of 2-Pyridone with Maleimide through Mn(I)-Catalyst: Migration of directing group through cleavage of C-N bond for the formation of all-carbon quaternary carbon center
Authors: Mohanty Smruti Ranjan , Prusty Namrata , Banjare Shyam Kumar , Nanda Tanmayee , Ravikumar Ponneri C.
Published: February 2022

An earth-abundant and inexpensive Mn(I)-catalyzed alkylation of 2-pyridone with maleimide has been reported for the first time, in contrast to previously reported Diels-alder product. The directing group was easily removed after functionalization. Notably, unexpected migration of pyridine ring has been discovered in presence of acetic acid, which also provides unique class of compounds with three different N-heterocycles with an all-carbon quaternary carbon center. Furthermore, single crystal X-ray and HRMS revealed a five-membered manganacycle intermediate. This methodology tolerates a wide variety of functional groups delivering the alkylated products in moderate to excellent yields.
Synovial Fluid Profile Dictates Nanopracticle Uptake into Cartilage- Implications of the Protein Corona for Novel Arthitis Treatments
Authors: von Mentzer Ula , Selldén Tilia , Råberg LOISE , Erensoy Gizem , Hultgård-Ekwall Anna-Karin , Stubelius Alexandra
Published: February 2022

A major obstacle for joint drug delivery is to penetrate the dense, negatively charged cartilage matrix. Previous studies have extensively investigated particle approaches to cartilage tissue uptake but have neglected to address potential interactions between the particles and the synovial fluid. Here, a NP panel with different PEGylation were incubated with synovial fluid from either rheumatoid or osteoarthritic patients, or FCS. Compared to non-protein covered NPs, we observed a prominent impact of the protein coronas on NP uptake into cartilage, chondrocytes, and monocytes. Utilizing a quantitative proteomics approach, we identified abundant proteins on all panel members irrespective of the NP modifications. Nonetheless, NP and protein condition-specific differences were also observed between the groups. Our study, therefore, suggests that the protein abundance dictates NP efficacy, emphasizing the importance of considering the biological milieu for translating drug delivery designs to the clinic.
Optical Nature of Non-Substituted Triphenylmethyl Cation: Crystalline State Emission, Thermochromism, and Phosphorescence
Authors: Nishiuchi Tomohiko , Sotome Hikaru , Fukuuchi Risa , Kamada Kenji , Miyasaka Hiroshi , Kubo Takashi
Published: February 2022

Since the discovery of the triphenylmethyl (trityl) cation 120 years ago, a variety of aromatic cations having various colors and luminescence properties have been rigorously studied. Many, differently substituted trityl cations have been synthesized and their optical properties have been elucidated. However, the optical properties of the parent, non-substituted and highly reactive trityl cation, which was observed to be very weakly luminescent, have not been subjected to detailed investigation. In the effort described herein, we explored the optical nature of non-substituted trityl hexafluorophosphate (PF6) in the crystalline state. Trityl PF6 was found to exist as two crystal polymorphs including a yellow (Y) and an orange (O) form. Moreover, we observed that these crystalline forms display crystalline-state emission with different colors. The results of X-ray crystallographic analysis showed that the two polymorphs have totally different molecular packing arrangements. Furthermore, an investigation of their optical properties revealed that the O-crystal undergoes a distinct color change to yellow upon cooling as a consequence of a change in the nature of the charge transfer interaction between the cation and PF6 anion, and that both the Y and O crystal forms phosphoresce.
Optical Nature of Non-Substituted Triphenylmethyl Cation: Crystalline State Emission, Thermochromism, and Phosphorescence
Authors: Nishiuchi Tomohiko , Sotome Hikaru , Fukuuchi Risa , Kamada Kenji , Miyasaka Hiroshi , Kubo Takashi
Published: February 2022

Since the discovery of the triphenylmethyl (trityl) cation 120 years ago, a variety of aromatic cations having various colors and luminescence properties have been rigorously studied. Many, differently substituted trityl cations have been synthesized and their optical properties have been elucidated. However, the optical properties of the parent, non-substituted and highly reactive trityl cation, which was observed to be very weakly luminescent, have not been subjected to detailed investigation. In the effort described herein, we explored the optical nature of non-substituted trityl hexafluorophosphate (PF6) in the crystalline state. Trityl PF6 was found to exist as two crystal polymorphs including a yellow (Y) and an orange (O) form. Moreover, we observed that these crystalline forms display crystalline-state emission with different colors. The results of X-ray crystallographic analysis showed that the two polymorphs have totally different molecular packing arrangements. Furthermore, an investigation of their optical properties revealed that the O-crystal undergoes a distinct color change to yellow upon cooling as a consequence of a change in the nature of the charge transfer interaction between the cation and PF6 anion, and that both the Y and O crystal exhibit phosphorescence.
Super-bridging Fibrous Materials for Water Treatment: Impacts on Removal of Plastic Particles, Phosphorus and Natural Organic Matter
Authors: Lapointe Mathieu , Jahandideh Heidi , Farner Jeffrey , Tufenkji Nathalie
Published: February 2022

Aggregation combined with gravitational separation is the most commonly used method to treat water globally, but it carries a significant economic and environmental burden as the chemicals used in the process (e.g., coagulants) generate ~8 million tons of metal-based sludge waste annually. To simultaneously deal with the issues of process sustainability, cost, and efficiency, we developed materials reengineered from pristine or waste fibers to serve as super-bridging agents, adsorbents, and ballast media. This study shows that these sustainable fiber-based materials considerably increased the floc size (~6630 µm) compared to conventional physicochemical treatment using a coagulant and a flocculant (~520 µm). The fiber-based materials also reduced coagulant (up to 40%) and flocculant usage (up to 60%). Moreover, the unprecedented size of flocs produced using fiber-based materials (up to ~13 times larger compared to conventional treatment) enabled easy floc removal by screening, thereby eliminating the need for a settling tank, a large and costly process unit. Our results show that fiber-based materials can be effective solutions at removing classical (e.g., natural organic matter (NOM) and phosphorus) and emerging contaminants (e.g., microplastics and nanoplastics). Due to their large size (> 3000 µm), some Si-grafted and Fe-grafted fiber-based materials can be easily recovered from settled/screened sludge and reused multiple times for coagulation/flocculation. Our results also show that these materials could be used in synergy with coagulants and flocculants to improve settling in existing water treatment processes. Furthermore, these reusable materials combined with separation via screening could allow global water treatment facilities to reduce their capital and operating costs as well as their environmental footprint.
Conversion of carboxylic acids to potassium acyltrifluoroborates (KATs) by Cu-catalyzed borylation of mixed anhydrides
Authors: Tung Pinku , Schuhmacher Anne , Schilling Philipp , Bode Jeffrey , Mankad Neal
Published: February 2022

We report the preparation of potassium acyltrifluoroborates (KATs) from widely-available carboxylic acids. Mixed anhydrides of carboxylic acids were prepared using isobutyl chloroformate and transformed to the corresponding KATs using a commercial copper catalyst, B2(pin)2 and aqueous KHF2. This method allows for the facile preparation of aliphatic, aromatic, and amino acid-derived KATs and is compatible with a variety of functional groups including alkenes, esters, halides, nitriles, and protected amines.