bluuebunny/crossref_metadata_2025 huggingface dataset:
Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE
Authors: Kovacs David Peter , van der Oord Cas , Kucera Jiri , Allen Alice , Cole Daniel , Ortner Christoph , Csanyi Gabor
Published: February 2022

We demonstrate that fast and accurate linear force fields can be built for molecules using the Atomic Cluster Expansion (ACE) framework. The ACE models parametrize the Potential Energy Surface in terms of body ordered symmetric polynomials making the functional form reminiscent of traditional molecular mechanics force fields. We show that the 4 or 5-body ACE force fields improve on the accuracy of the empirical force fields by up to a factor of 10, reaching the accuracy typical of recently proposed machine learning based approaches. We not only show state of the art accuracy and speed on the widely used MD17 and ISO17 benchmark datasets, but also go beyond RMSE by comparing a number of ML and empirical force fields to ACE on more important tasks such as normal mode prediction, high temperature molecular dynamics, dihedral torsional profile prediction and even bond breaking. We also demonstrate the smoothness, transferability and extrapolation capabilities of ACE on a new challenging benchmark dataset comprising a potential energy surface of a flexible drug-like molecule.
PRISMA: A robust and intuitive tool for high-throughput processing of chemical spectra
Authors: Flores Eibar , Mozhzhukhina Nataliia , Li Xinyu , Norby Poul , Matic Aleksandar , Vegge Tejs
Published: February 2022

The popularization of high-throughput spectroscopies to characterize functional materials requires the simultaneous development of new analysis tools to efficiently process large numbers of measurements into scientifically meaningful observables. Here we introduce PRISMA, an open-source tool to rapidly analyze hundreds of spectra in a semi-automated way. PRISMA follows a human-in-the-loop workflow, where the user interacts with an intuitive graphical user interface (GUI) to control multiple steps in the spectrum analysis process: trimming, baseline correction, and peak fitting. The user tunes the analysis in real-time and applies the optimal parameters to all spectra, outputting processed results in an easy-to-read csv format within seconds. Crucially, the tuned parameters are stored to guarantee the full reproducibility of the analysis. We describe the functionalities implemented in PRISMA and test its capabilities with three experimental cases relevant to the study of electrochemical energy storage and conversion devices: temperature-dependent Raman measurement of phase transitions, a linear Raman mapping of a graphite composite electrode, and an operando X-ray diffraction experiment of LiNiO2 Li-ion electrode. Even if X-ray diffraction is not a spectroscopic technique, diffraction patterns are represented as one-dimensional arrays of counts equally suitable for analysis with PRISMA. The case studies demonstrate the robustness of the app and its ability to unearth insightful trends in peak parameters, which are easier to represent, interpret and further analyze with more advanced techniques.
Superatomic Au25(SC2H5)18 Nanocluster under Pressure
Authors: Tang Qing , Li Fuhua , Jiang De-en
Published: February 2022

The last decade has witnessed significant advances in the synthesis and structure determination of atomically precise metal nanoclusters. However, little is known about the condensed matter properties of these nanosized metal nanoclusters packed in a crystal lattice under high pressure. Here using density function theory calculations, we simulate the crystal of a representative superatomic gold cluster, [Au25(SR)18]0 (R = C2H5), under various pressures. At ambient conditions, [Au25(SC2H5)18]0 clusters are packed in a crystal via dispersion interactions; being a 7e superatom, each cluster carries a magnetic moment of 1μB or one unpaired electron. Upon increasing compression (from 10 to 110 GPa), we observe the formation of inter-cluster Au-Au, Au-S, and S-S covalent bonds between staple motifs, thereby linking the clusters into a network. The pressure-induced structural change is accompanied by the vanishment of the magnetic moment and the semiconductor-to-metal transition. Our work shows that subjecting crystals of atomically precise metal nanoclusters to high pressures could lead to new crystalline states and physical properties.
Mechanism of Ammonia Oxidation to Dinitrogen, Nitrite, and Nitrate on 𝛽-Ni(OH)2 from First-Principles Simulations
Authors: Choueiri Rachelle M. , Tatarchuk Stephen W. , Klinkova Anna , Chen Leanne D.
Published: February 2022

The electrocatalyzed ammonia oxidation reaction (AOR) is a potential pathway toward waste ammonia remediation, energy generation, and the synthesis of value- added products. To date, mechanistic studies have focused on elucidating the progress of AOR on Pt-based catalysts with an established pathway for N2 only. In this work, density functional theory was applied to determine the lowest energy intermediates towards nitrogen gas, nitrite, and nitrate formation on 𝛽-Ni(OH)2, a promising electrocatalyst material for AOR. It was found that dinitrogen formation progresses via NH-NH coupling while nitrite and nitrate formation occurs via deprotonation to adsorbed N and subsequent hydroxylation to form oxygenated intermediates. This work is the first to report a mechanism for nitrite and nitrate formation and will also serve as a benchmark for future studies on Ni-based materials.
In-situ fabrication of metal oxide nanocaps based on biphasic reactions with surface nanodroplets
Authors: Wei Zixiang , Dabodiya Tulsi , Chen Jian , Lu Qiuyun , Qian Jiasheng , Meng Jia , Zeng Hongbo , Qian Hui , Zhang Xuehua
Published: February 2022

Surface-bound nanomaterials are widely used in clean energy techniques from lithium batteries, solar-driven evaporation in desalination to hydrogen production by photocatalytic electrolysis. Reactive surface nanodroplets may potentially streamline the process of fabrication of a range of surface-bound nanomaterials invoking biphasic reactions at interfaces. In this work, we demonstrate the feasibility of reactive surface nanodroplets for in-situ synthesis and anchoring of nanocaps of metal oxides with tailored porous structures. Spatial arrangement and surface coverage of nanocaps are predetermined during the formation of reactive nanodroplets, while the crystalline structures of metal oxides can be controlled by thermal treatment of organometallic nanodroplets produced from the biphasic reactions. Notably, tuning the ratio of reactive and non-reactive components in surface nanodroplets enables the formation of porous nanocaps that can double photocatalytic efficiency in the degradation of organic contaminants in water, compared to smooth nanocaps. In total, we demonstrate in-situ fabrication of four types of metal oxides in the shape of nanocaps. Our work shows that reactive surface nanodroplets may open a door to a general, fast and tuneable route for preparing surface-bound metal oxides. This fabrication approach may help develop new nanomaterials needed for photocatalytic reactions, wastewater treatment, optical focusing, solar energy conversion and other clean energy techniques.
Least-Squares Fitting of Multidimensional Spectra to Kubo Lineshape Models
Authors: Robben Kevin , Cheatum Christopher
Published: February 2022

We report a comprehensive study of the efficacy of least-squares fitting of multidimensional spectra to generalized Kubo lineshape models and introduce a novel least-squares fitting metric, termed the Scale Invariant Gradient Norm (SIGN), that enables a highly reliable and versatile algorithm. The precision of dephasing parameters is between 8× to 50× better for nonlinear model fitting compared to the CLS method, which effectively increases data acquisition efficiency by one to two orders of magnitude. Whereas the center-line-slope (CLS) method requires sequential fitting of both the nonlinear and linear spectra, our model fitting algorithm only requires nonlinear spectra, but accurately predicts the linear spectrum. We show an experimental example in which the CLS time constants differ by 60% for independent measurements of the same system, while the Kubo time constants differ by only 10% for model fitting. This suggests that model fitting is a far more robust method of measuring spectral diffusion than the CLS method, which is more susceptible to structured residual signals that are not removable by pure solvent subtraction. Statistical analysis of the CLS method reveals a fundamental oversight in accounting for the propagation of uncertainty by Kubo time constants in the process of fitting to the linear absorption spectrum. A standalone desktop app and source code for the least-squares fitting algorithm are freely available with example lineshape models and data. We have written the MATLAB source code in a generic framework where users may supply custom lineshape models. Using this application, a standard desktop fits a 12-parameter generalized Kubo model to a 106 data-point spectrum in a few minutes.
Enhancement of photoacoustic spectroscopy with sorption enrichment for ppt-level benzene detection
Authors: Karhu Juho , Hieta Tuomas
Published: February 2022

A real time trace gas detector for benzene is demonstrated. The measurement system takes an advantage of modest enrichment through short adsorption periods to reach a ppt-level detection limit with a sampling cycle of 90 s, which includes sample adsorption, desorption and a spectroscopic measurement. Benzene is collected on Tenax TA sorbent for 30 s and then detected from the enriched samples with photoacoustic spectroscopy. A high sensitivity is achieved using cantilever-enhanced photoacoustic spectroscopy and a continuous-wave quantum cascade laser emitting at the wavelength 14.8 μm, which corresponds to the absorption wavelength of the strongest benzene infrared band. We reach a detection limit of 150 ppt of benzene, over one sampling cycle. Interference from humidity and other common petrochemicals is evaluated.
Structural Dynamics and Thermal Transport in Bismuth Chalcogenide Alloys
Authors: Cen Jiayi , Pallikara Ioanna , Skelton Jonathan
Published: February 2022

We present a detailed study of the structural dynamics, energetic and dynamical stability and thermal transport of the bismuth chalcogenides Bi2S3, Bi2Se3 and Bi2Te3 and their alloys. The differing activities of the Bi cation lone pairs in Bi2S3, Bi2Se3 and Bi2Te3 lead to competition between orthorhombic Pnma and rhombohedral R-3m phases, with the latter favored by heavier chalcogen atoms, while the reported non-ambient phases of Bi2Se3 and Bi2Te3 show phonon instabilities under ambient conditions. The Pnma structure has weaker chemical bonding and stronger phonon anharmonicity than the R-3m phase, resulting in an intrinsically lower lattice thermal conductivity. A thermodynamic model of Bi2[Se(1-x)S(x)]3 indicates that the R-3m structure is energetically favored only for low S content, but the stability window can potentially be extended at lower formation temperatures. Bi2[Se(1-x)Te(x)]3 in the R-3m phase shows substantial deviation from ideal solid-solution behavior, due to a strong energetic preference for the Se and Te atoms to occupy the interior and exterior sites, respectively, in the constituent quintuple layers. Strain-field fluctuations induced by inhomogeneities in the chemical bonding are shown to play a significant role in determining the heat transport in the alloy systems, and chalcogen disorder away from the preferred symmetric structure is found to be an important factor in the reduced thermal conductivity of Bi2SeTe2 compared to the Bi2Te3 endpoint. The microscopic insight from these modelling studies provides new insight into the bismuth chalcogenides and their alloys, which may inform ongoing research to optimize the thermoelectric performance of these and related materials.
Iron Catalyzed C-C Single Bond Cleavage of Alcohols
Authors: Liu Wei , Wu Qiang , Wang Miao , Huang Yahao , Hu Peng
Published: February 2022

An iron-catalyzed deconstruction/hydrogenation reaction of alcohols through C-C bond cleavage is developed under the irradiation of visible light, to produce ketones or aldehydes as the products. Linear alcohols and cycloalkanols with different ring sizes are suitable substrates, containing tertiary, secondary, and primary alcohols bearing a wide range of substitutes. Complex natural alcohols can also perform the transformation selectively. The mechanism investigation reveals an unpresented reaction procedure that involves chlorine radical as a key intermediate, which is generated from [FeCl4]- through ligand to metal charge transfer (LMCT). The study illustrates new possibilities for iron photocatalysis, especially for various deconstruction/functionalization reactions.
Understanding the Origins of Changing the Product Specificity Properties of Arginine Methyltransferase PRMT7 by E181→D and E181→D/Q329→A Mutations: A QM/MM Study
Authors: Ren Wan-Sheng , Rahman Adua , Jiang Kai-Bin , Deng Hao , Zhao Yuan-Yuan , Zhang Wei-Jie , Liu Kedian , Qian Ping , Guo Hong
Published: February 2022

Arginine methylations can regulate important biological processes and affect many cellular activities, and the enzymes that catalyze the methylations are protein arginine methyltransferases (PRMTs). The biological consequences of arginine methylations depend on the methylation states of arginine that are determined by the PRMT’s product specificity. Although the product specificity is a very important property, it is still unknown concerning why different PRMTs may generate different methylation states for the target arginine residues on protein substrates. PRMT7 is the only known member of Type III PRMT that produces mono-methylarginine (MMA) product. Interestingly, its E181D and E181D/Q329A mutants can catalyze, respectively, the formation of asymmetrically di-methylated arginine (ω-NG, NG-dimethylarginine or ADMA) and symmetrically di-methylated arginine (ω-NG, N'G-dimethylarginine or SDMA). The exact reasons for such product specificity modification as a result of the mutations have been unclear. Here QM/MM molecular dynamics (MD) and potential of mean force (PMF) free-energy simulations are performed for the E181D and E181D/Q329A mutants to understand the catalytic mechanism and the origin of their different product specificities from that of the wild-type PRMT7 as well as between E181D and E181D/Q329A. The simulations show that while the free energy barriers of E181D and E181D/Q329A for the first methylation are higher than that of the wild type, E181D and E181D/Q329A have the ability to add the second methyl group to the target mono-methyl arginine and generate ADMA and SDMA, respectively. The free energy barriers for E181D and E181D/Q329A to produce ADMA and SDMA, respectively, are considerably lower than the corresponding barriers involving the wild-type enzyme. Moreover, the computational study identifies some important structural, electronic and dynamic features that lead to the different product specificities and activities of the wild-type PRMT7, E181D and E181D/Q329A. These factors may play important roles in controlling the activity and product specificity of other PRMTs as well.
Structural and Electronic Effects of X-ray Irradiation on Prototypical [M(COD)Cl]2 Catalysts
Authors: Fernando Nathalie , Cairns Andrew B. , Murray Claire A. , Thompson Amber L. , Dickerson Joshua L. , Garman Elspeth F. , Ahmed Nayera , Ratcliff Laura E. , Regoutz Anna
Published: February 2022

X-ray characterisation techniques are invaluable for probing material characteristics and properties, and have been instrumental in discoveries across materials research. However, there is a current lack of understanding of how X-ray induced effects manifest in small molecular crystals. This is of particular concern as new X-ray sources with ever increasing brilliance are developed. In this paper, systematic studies of X-ray-matter interactions are reported on two industrially important catalysts, [Ir(COD)Cl]2 and [Rh(COD)Cl]2, exposed to radiation in X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) experiments. From these complimentary techniques, changes to structure, chemical environments, and electronic structure are observed as a function of X-ray exposure, allowing comparisons of stability to be made between the two catalysts. Radiation dose is estimated using recent developments to the RADDOSE-3D software for small molecules and applied to powder XRD and XPS experiments. Further insights into the electronic structure of the catalysts and changes occurring as a result of the irradiation are drawn from density functional theory (DFT). The techniques combined here offer much needed insight into the X-ray induced effects in transition metal catalysts and consequently, their intrinsic stabilities. There is enormous potential to extend the application of these methods to other small molecular systems of scientific or industrial relevance.
Direct and Catalytic C-Glycosylation of Arenes: Expeditious Synthesis of the Remdesivir Nucleoside
Authors: Obradors Carla , Mitschke Benjamin , Aukland Miles H. , Leutzsch Markus , Grossmann Oleg , Brunen Sebastian , Schwengers Sebastian A. , List Benjamin
Published: February 2022

Since early 2020, scientists have strived to find an effective solution to fight SARS-CoV-2, especially by developing reliable vaccines that inhibit the spread of the disease and repurposing drugs for combatting its effects on the human body. The antiviral prodrug remdesivir is still the most widely used therapeutic during the early stage of the infection. However, the current synthetic routes rely on the use of protecting groups, air-sensitive reagents, and cryogenic conditions, impeding the cost-efficient supply to patients. We therefore focused on the development of a straightforward, direct addition of (hetero)arenes to unprotected sugars. Here we report a silylium-catalyzed and completely stereoselective C-glycosidation that initially yields the open-chain polyols, which can be selectively cyclized to provide either the kinetic alpha-furanose or the thermodynamically favored beta-anomer. The method significantly expedites the synthesis of remdesivir precursor GS-441524 after subsequent Mn-catalyzed C–H oxidation and deoxycyanation.
Structural Diversity of Lanthanide 3-Nitrotrispyrazolylborates: Tunable Nuclearity and Intra-Ligand Charge Transfer Sensitization of Visible and NIR Ln3+ Emission
Authors: Hossack Christopher H. , Butcher Raymond J. , Cahill Christopher L. , Besson Claire
Published: February 2022

Reported are the synthesis, crystal structures and photophysical properties of twenty-eight, novel lanthanide compounds across five structural types, [Ln(3-NO2Tp)2(NO3)] (1-Ln, Ln = La – Tm, except Pm), [Bu4N][Ln(3-NO2Tp)(NO3)3] (2-Ln, Ln = Yb, Lu), [Eu(3-NO2Tp)2Cl(H2O)]·2iPrOH (3-Eu), [{Ln(3-NO2Tp)2}2(μ2-CO3)] (4-Ln, Ln = La – Gd, except Pm) and [{Ln(3-NO2Tp)}4(μ2-OMe)6(μ4-O)] (5-Ln, Ln = Pr – Tb, except Pm) with the 3-nitrotrispyrazolylborate (3-NO2Tp–) ligand. Reaction of methanol or isopropanol solutions of LnX3 (X = Cl, NO3) with the tetrabutyl ammonium salt of the flexidentate 3-NO2Tp–, ([Bu4N][3-NO2Tp]) yields Ln(3-NO2Tp)x complexes of various nuclearities as either monomers (1-Ln, 2-Ln, 3-Eu), dimers (4-Ln) or tetramers (5-Ln) owing to the efficient conversion of atmospheric CO2 to CO32– (dimers) or ligand controlled solvolysis of lanthanide ions (tetramers). 3-NO2Tp– is an efficient sensitizer for both the visible and near-IR (NIR) emissions of most of the lanthanide series, except thulium. Optical measurements, supported by density functional theory calculations, indicate that the dual visible and NIR Ln3+ emission arises from two intra-ligand charge transfer (ILCT) transitions of 3-NO2Tp–. This is the first report of lanthanide complexes with a nitro-functionalized pyrazolylborate ligand. The derivatization of the known Tp– ligand results in new coordination chemistry governed by the increased denticity of 3-NO2Tp–, imparting remarkable structural diversity and charge transfer properties to resultant lanthanide complexes.
Unbinding of hACE2 and Inhibitors from the Receptor Binding Domain of SARS-CoV-2 Spike Protein
Authors: Mishra Lokpati , Bandyopadhyay Tusar
Published: February 2022

The first direful biomolecular event leading to COVID-19 disease is the SARS-CoV-2 virus surface spike (S) protein-mediated interaction with the human transmembrane protein, angiotensin-converting enzyme 2 (hACE2). Prevention of this interaction presents an attractive alternative to thwart SARS-CoV-2 replications. The development of monoclonal antibodies (mAbs) in the convalescent plasma treatment, nanobody, and designer peptides, which recognizes epitopes that overlap with hACE2 binding sites in the receptor-binding domain (RBD) of S protein (S/RBD) and thereby blocking the infection has been the center stage of therapeutic research. Here we report atomistic and reliable in silico structure-energetic features of the S/RBD interactions with hACE2 and its two inhibitors (convalescent mAb, B38, and an alpaca nanobody, Ty1). The discovered potential of mean forces exhibits free energy basin and barriers along the interaction pathways, providing sufficient molecular insights to design a B38 mutant and a Ty1-based peptide with higher binding capacity. While the mutated B38 forms a 60-fold deeper free energy minimum, the designer peptide (Ty1-based) constitutes 38 amino acids and is found to form a 100-fold deeper free energy minimum in the first binding basin than their wild-type variants in complex with S/RBD. Our strategy may help to design more efficacious biologics towards therapeutic intervention against the current raging pandemic.
An Expedited Phenotypic Approach Towards Organic Reaction Generality
Authors: Prieto Kullmer Cesar N. , Kautzky Jacob A. , Krska Shane W. , Nowak Timothy , Dreher Spencer D. , MacMillan David W. C.
Published: February 2022

Reaction generality is crucial in determining the overall impact and usefulness of organic synthetic methods. In contrast, contemporary generalization processes seem unable to meet the growing demand for robust methodology. We sought to develop an accelerated approach towards achieving generality, inspired by phenotypic screening, that rapidly expands the scope and utility of synthetic methods. This approach was validated by example of the metallaphotoredox decarboxylative arylation, resulting in the discovery of a novel additive that overcomes many lingering limitations of this method and has significant mechanistic implications for nickel-catalyzed cross couplings in general.
Adsorbate chemical environment-based machine learning framework for heterogeneous catalysis
Authors: Ghanekar Pushkar , Deshpande Siddharth , Greeley Jeffrey
Published: February 2022

Heterogeneous catalytic reactions are influenced by a subtle interplay of atomic-scale factors, ranging from the catalysts’ local morphology to the presence of high adsorbate coverages. Describing such phenomena via computational models requires generation and analysis of a large space of surface atomic configurations. To address this challenge, we present the Adsorbate Chemical Environment-based Graph Convolution Neural Network (ACE-GCN), a screening workflow that can account for atomistic configurations comprising diverse adsorbates, binding locations, coordination environments, and substrate morphologies. Using this workflow, we develop catalyst surface models for two illustrative systems: (i) NO adsorbed on a Pt3Sn(111) alloy surface, of interest for nitrate electroreduction processes, where high adsorbate coverages combine with the low symmetry of the alloy substrate to produce a large configurational space, and (ii) OH* adsorbed on a stepped Pt(221) facet, of relevance to the Oxygen Reduction Reaction, wherein the presence of irregular crystal surfaces, high adsorbate coverages, and directionally-dependent adsorbate-adsorbate interactions result in the configurational complexity. In both cases, the ACE-GCN model, having trained on a fraction (~10%) of the total DFT-relaxed configurations, successfully ranks the relative stabilities of unrelaxed atomic configurations sampled from a large configurational space. This approach is expected to accelerate development of rigorous descriptions of catalyst surfaces under in-situ conditions.
Biocatalytic One-Carbon Ring Expansion of Aziridines to Azetidines via a Highly Enantioselective [1,2]-Stevens Rearrangement
Authors: Miller David , Lal Ravi , Marchetti Luca , Arnold Frances
Published: February 2022

We report enantioselective one-carbon ring expansion of aziridines to make azetidines as a new-to-nature activity of engineered ‘carbene transferase’ enzymes. A laboratory-evolved variant of cytochrome P450BM3, P411-AzetS, not only exerts unparalleled stereocontrol (99:1 er) over a [1,2]-Stevens rearrangement, but also overrides the inherent reactivity of aziridinium ylides, cheletropic extrusion of olefins, to perform a [1,2]-Stevens rearrangement. By controlling the fate of the highly reactive aziridinium ylide intermediates, these evolvable biocatalysts promote a transformation which cannot currently be performed using other catalyst classes.
Unveiling the Fluorescence Origin in Pyrene Derived Graphene Quantum Dots: A Single Particle Level Analysis
Authors: Batra Gayatri , Sharma Shubham , Kaushik Kush , Rao Chethana , Kumar Pawan , Kumar Krishan , Ghosh Subrata , Jariwala Deep , Stach Eric A. , Yadav Aditya , Nandi Chayan Kanti
Published: February 2022

The bottom-up approach has been the preferred route for large-scale synthesis of graphene quantum dots (GQDs). However, the structure and origin of photoluminescence in these dots synthesized by the bottom-up approach are still a subject of debate. Here, using a series of separation techniques like solvent extraction, column chromatography, gel electrophoresis and dialysis, we present three distinct fluorescent materials in GQDs synthesized from pyrene, a well-known precursor molecule. The subtle balance between the extent of graphitization and molecular fluorophores determines the nature of fluorescence emission in GQDs verified using a suite of optical and vibrational spectroscopy techniques in combination with electron microscopy. The single-particle level emission properties strongly support our observation. Using cell imaging studies, we also verify that all three materials are suitable for fluorescent staining of biological samples. Our results resolve a long-standing debate on the true structural character of GQDs and their source of emission.
Toward sustainable syntheses of Ca-based MOFs
Authors: Crickmore Tom , Begum Sana Haamidah , Mitchell Hannah , Clark Molly , Bradshaw Darren
Published: February 2022

We report the use of benign and green precursors, including waste chicken eggshells and PET (polyethyleneterephthalate) from recycled plastic bottles, for the facile synthesis of a variety of calcium-based metal-organic frameworks (Ca-MOFs), using water based and mechanochemical synthesis techniques.
Simple Nonionic Omnisoluble Tetraphenylporphyrin for Relative Referencing of Singlet Oxygen Quantum Yield
Authors: Payne Daniel T. , Hynek Jan , Labuta Jan , Hill Jonathan P.
Published: February 2022

Meso-tetrakis-(3,4,5-tris{2-[2-(2-methoxyethoxy)ethoxy]ethoxy}phenyl)porphyrin TEG12PH2 is reported as an ‘omnisoluble’ TPP reference for singlet oxygen (1O2) generation quantum yield (ΦSO) estimation. TEG12PH2 is a highly soluble, nonionic compound possessing excellent 1O2 QY in a wide variety of common solvents, including water. TEG12PH2 was prepared on multigram scale by the 12-way O-alkylation of tetrakis(3,4,5-trihydroxyphenyl)porphyrin using 2-(2-(2-methoxyethoxy)ethoxy)ethyl 4-toluenesulfonate as reaction solvent. The corresponding Zn(II) complex TEG12PZn was also prepared and studied. Its 1O2 QYs in the different solvents studied were found to be 0.86 (acetone), 0.59 (acetonitrile), 0.66 (chloroform), 0.85 (methanol), 0.45 (toluene) and 0.51 (water). TEG12PH2 can be considered a reliable and easy to implement omnisoluble reference compound for the estimation of the 1O2 generating activities of new materials, especially new porphyrinic compounds.
A microfluidic system for analysis of electrochemical processing using a highly sensitive optical fiber microcavity and a microfluidic system
Authors: Krześniak Andrzej , Gabler Tomasz , Janik Monika , Koba Marcin , Jönsson-Niedziółka Martin , Śmietana Mateusz
Published: February 2022

Microfluidics provide unique possibilities to control tiny volumes of liquids and their composition. To effectively benefit from the advantages of microfluidic solutions they need to be supported by interrogation subsystems, at best also matching the miniature scale. In this work we combined with a microfluidic system a Microcavity in-line Mach-Zehnder Interferometer (µIMZI) induced in the side surface of a single-mode optical fiber using a femtosecond laser micromachining. The µIMZI shows capability for investigating optical properties of as small as picoliter volumes with an exceptionally high sensitivity. Here we report numerical analysis and experimental results that show that when the µIMZI is incorporated with the microfluidic system the measurements can be performed with sensitivity exceeding 14,000 nm/RIU which is similar to measurements done under static conditions. In a flow injection system we show that a certain amount of liquid and flow rate are required to effectively exchange the liquid in the microcavity, while orientation of the cavity versus the flow direction has a minor impact on the exchange. Finally, we have supported the system by band electrodes making it possible to induce redox reactions in the microchannel and optical detection of flowing products of the reactions. It has been found that thanks to the high sensitivity of the µIMZI the products of the reactions can be clearly detected both electrochemically and optically even when the only part of the flowing redox probe is oxidized at the band electrode. This work proves that the proposed solution may offer highly sensitive optical measurements, even when the chemical reactions are not effective in the whole volume of the system.
A microfluidic system for analysis of electrochemical processing using a highly sensitive optical fiber microcavity
Authors: Krześniak Andrzej , Gabler Tomasz , Janik Monika , Koba Marcin , Jönsson-Niedziółka Martin , Śmietana Mateusz
Published: February 2022

Microfluidics provide unique possibilities to control tiny volumes of liquids and their composition. To effectively benefit from the advantages of microfluidic solutions they need to be supported by interrogation subsystems, at best also matching the miniature scale. In this work we combined with a microfluidic system a Microcavity in-line Mach-Zehnder Interferometer (µIMZI) induced in the side surface of a single-mode optical fiber using a femtosecond laser micromachining. The µIMZI shows capability for investigating optical properties of as small as picoliter volumes with an exceptionally high sensitivity. Here we report numerical analysis and experimental results that show that when the µIMZI is incorporated with the microfluidic system the measurements can be performed with sensitivity exceeding 14,000 nm/RIU which is similar to measurements done under static conditions. In a flow injection system we show that a certain amount of liquid and flow rate are required to effectively exchange the liquid in the microcavity, while orientation of the cavity versus the flow direction has a minor impact on the exchange. Finally, we have supported the system by band electrodes making it possible to induce redox reactions in the microchannel and optical detection of flowing products of the reactions. It has been found that thanks to the high sensitivity of the µIMZI the products of the reactions can be clearly detected both electrochemically and optically even when the only part of the flowing redox probe is oxidized at the band electrode. This work proves that the proposed solution may offer highly sensitive optical measurements, even when the chemical reactions are not effective in the whole volume of the system.
Highly efficient water oxidation via a bimolecular reaction mechanism on rutile structured mixed-metal oxyfluorides
Authors: Gohari-Bajestani Zahra , Wang Xiao , Guiet Amandine , Moury Romain , Grenèche Jean-Marc , Hémon-Ribaud Annie , Zhang Yuxuan , Chartrand Daniel , Maisonneuve Vincent , Seifitokaldani Ali , Kornienko Nikolay , Lhoste Jérôme
Published: February 2022

Mixed-metal oxides are generally considered to be the highest-performance catalysts for alkaline water oxidation. Despite significant efforts dedicated to understanding and accelerating their efficiency, most works have been limited investigations of Ni, Co, and Fe oxides, thus overlooking beneficial effects of hetero-anion incorporation. To this end, we report on the development of Co0.5Fe0.5O0.5F1.5 oxyfluoride materials featuring a rutile crystal structure and porous morphology via a scalable and green synthetic route. The catalyst surface, enhanced through electron withdrawing effects imparted by the fluoride ions, give rise to highly effective catalytic sites for electrochemical water oxidation. In particular, their performance across metrics of Tafel slope (27 mV/dec), mass activity (846 A/g at 1.53 V vs. RHE), turnover frequency (21/s at 1.53 V vs. RHE), overpotential (220 mV for 10 mA/cm2), and stability (27 days of continuous operation) largely surpasses most known Co-based catalysts. Mechanistic studies suggest that this performance is driven by a bimolecular, oxygen coupling reaction mechanism through proximal active sites on the catalyst surface, thus enabling a new avenue for achieving accelerated oxygenic electrocatalysis.
Elucidating the Dynamics of Polymer Transport through Nanopores using Asymmetric Salt Concentrations
Authors: Charron Martin , Philipp Lucas , He Liqun , Tabard-Cossa Vincent
Published: February 2022

While notable progress has been made in recent years both experimentally and theoretically in understanding the highly complex dynamics of polymer capture and transport through nanopores, there remains significant disagreement between experimental observation and theoretical prediction that needs to be resolved. Asymmetric salt concentrations, where the concentrations of ions on each side of the membrane are different, can be used to enhance capture rates and prolong translocation times of polymers translocating through a nanopore from the low salt concentration reservoir, which are both attractive features for single-molecule analysis. However, since asymmetric salt concentrations affect the electrophoretic pull inside and outside the pore differently, it also offers a useful control parameter to elucidate the otherwise inseparable physics of the capture and translocation process. In this work, we attempt to paint a complete picture of the dynamics of polymer capture and translocation in both symmetric and asymmetric salt concentration conditions by reporting the dependence of multiple translocation metrics on voltage, polymer length, and salt concentration gradient. Using asymmetric salt concentration conditions, we experimentally observe the predictions of tension propagation theory and verify the significant impact of the electric field gradient on pre-stretching polymers on approach to the pore.
SuFEx-Enabled, Chemoselective Synthesis of Triflates, Triflamides and Triflimidates
Authors: Li Bing-Yu , Voets Lauren , Van Lommel Ruben , Hoppenbrouwers Fien , Alonso Mercedes , Verhelst Steven H. L. , De Borggraeve Wim M. , Demaerel Joachim
Published: February 2022

Sulfur(VI) Fluoride Exchange (SuFEx) chemistry has emerged as a next-generation click reaction, designed to assemble functional molecules quickly and modularly. Here, we report the ex situ generation of trifluoromethanesulfonyl fluoride (CF3SO2F) gas in a two chamber system, and its use as a new SuFEx handle to efficiently synthesize triflates and triflamides. This broadly tolerated protocol lends itself to peptide modification or to telescoping into coupling reactions. Moreover, redesigning the SVI–F connector with a S=O → S=NR replacement, furnished the analogous triflimidoyl fluorides as SuFEx electrophiles, which were engaged in the synthesis of rarely reported triflimidate esters. Notably, experiments showed H2O to be the key towards achieving chemoselective trifluoromethanesulfonation of phenols vs. amine groups, a phenomenon best explained—using ab initio metadynamics simulations—by a hydrogen bonded termolecular transition state for the CF3SO2F triflylation of amines.
Potential Energy Curves of Molecular Nitrogen for Singly and Doubly Ionized States with Core and Valence Holes
Authors: Bhattacharya Debarati , Shamasundar K. R. , Emmanouilidou Agapi
Published: February 2022

Our manuscript, presents the computation of potential energy curves of all possible singly and doubly ionized states of molecular nitrogen. Accurate representation of the potential energy curves of ionized states of N2 is essential to explicitly treat coupled electron-nuclear dynamics. In this work, we compute the potential energy curves of the valence as well as the core and inner valence singly and doubly ionized states of N2. These curves pave way to study the interplay between photoionization and Auger spectra when molecular nitrogen interacts with free electron lasers.Computation of inner valence or core ionized potential energy curve is not trivial due to the well-known problem of variational collapse of the wavefunction to the lowest energy state. We circumvent this problem by implementing a two-step optimization scheme within the multi-configurational self-consistent field approach. Such a two-step optimization scheme has been previously implemented to compute potential energy curves of core ionized states of di-atomic molecules with one hole. Herein, we show the general applicability of this two-step optimization method by computing potential energy curves of both singly and doubly ionized states of N2 with valence and core holes. Calculation of potential energy curves for core ionized polyatomic systems are scarce. Moreover, our approach is system independent and can be easily extended to calculate multiple-core ionized states. To the best of our knowledge, this is the first calculation of potential energy curves for doubly ionized states of a diatomic molecule with two core (or inner valence) holes.
Electronic Structure and Magnetism of Pristine, Defected, and Strained Ti2N MXene
Authors: Limbu Yogendra , Kaphle Gopi Chandra , Karn Alok Lal , Shah Niraj Kumar , Paudyal Durga
Published: February 2022

From first principles electronic structure calculations, we unravel the evolution of structural, electronic, and magnetic properties of pristine, defected, and strained titanium nitride MXene with different functional groups (-F, -O, -H, and -OH). The formation and cohesive energies reveal their chemical stability. The MAX phase and defect free functionalized MXenes are metallic except for oxygen terminated (Ti 2 NO 2 ) one which is 100% spin polarized half-metallic ferromagnet. The spin-orbit coupling significantly influences the bare MXene (Ti 2 N) to exhibit Dirac topology and band inversion near the high symmetry directions and Fermi level. The strain effect sways the Fermi level thereby shifting it toward lower energy state under compression and toward higher energy state under tensile strain in Ti 2 NH 2 . The Ti 2 NO 2 exhibits exotic electronic structure and magnetic states not only in pristine but also in strained and defected structures. Its half-metallic nature changes to semi-metallic under 1% compression and it is completely destroyed under 2% compression. In single vacancy defect, its band structure remarkably transforms from half-metallic to semi-conducting with large band gap in 12.5% Ti, weakly semi-conducting in 5.5% Ti, and semi-metallic in 12.5% O. The 25% N defect changes it’s half-metallic characteristic to metallic. Further, the 12.5% Co substitution preserves it’s half-metallic character, whereas Mn substitution allows it to convert half-metallic characteristic into weak semi-metallic characteristic preserving ferromagnetism. However, Cr substitution converts half-metallic ferromagnetic state to half-metallic anti-ferromagnetic state. The understanding made here on collective structural stability, and electronic band structure, and magnetic phenomena in novel 2D Ti 2 N derived MXenes open up their possibility in designing them for synthesis and thereby taking to applications.
Selective and stoichiometric incorporation of ATP by self-assembling amyloid fibrils.
Authors: Dec Robert , Puławski Wojciech , Dzwolak Wojciech
Published: February 2022

ATP acts as a biological hydrotrope preventing protein aggregation. Here, we report a novel chimeric peptide, ACC1-13K8, with an unusual capacity to bind and incorporate ATP while self-assembling into amyloid fibrils. The amino acid sequence combines highly amyloidogenic segment of insulin’s A-chain (ACC1-13) and octalysine (K8). Fibrillization requires binding 2 ATP molecules per ACC1-13K8 monomer and is not triggered by adenosine di- and monophosphates (ADP, AMP). Infrared and CD spectra and AFM-based morphological analysis reveal tight and orderly entrapment of ATP within superstructural hybrid peptide-ATP fibrils. The incorporation of ATP is an emergent property of ACC1-13K8 not observed for ACC1-13 and K8 segments separately. We demonstrate how new functionalities (e.g. ATP storage) emerge from synergistic coupling of amyloidogenic segments with non-amyloidogenic peptide ligands, and suggest that ATP’s role in protein misfolding is more nuanced than previously assumed.
Photoenzymatic Synthesis of 𝜶-Tertiary Amines By Engineered Flavin-Dependent ‘Ene’-Reductases
Authors: Gao Xin , Turek-Herman Joshua , Choi Young Joo , Cohen Ryan , Hyster Todd
Published: February 2022

𝛼-tertiary amines are a common motif in pharmaceutically important molecules but are challenging to prepare using asymmetric catalysis. Here, we demonstrate engineered flavin-dependent ‘ene’-reductases (EREDs) can catalyze radical additions into oximes to prepare this motif. Two different EREDs were evolved into competent catalysts for this transformation with high levels of stereoselectivity. Mechanistic studies indicate that the oxime contributes to the enzyme templated CT-complex formed between the substrate and cofactor. These products can be further deri-vatized to prepare a variety of motifs, highlighting the ver-satility of ERED photoenzymatic catalysis for organic syn-thesis.
Triplet-to-Singlet Exciton Transfer in Hyperfluorescent OLED materials
Authors: de Sousa Leonardo Evaristo , dos Santos Born Larissa , de Oliveira Neto Pedro Henrique , de Silva Piotr
Published: February 2022

Hyperfluorescent organic light-emitting diodes combine two kinds of dopants to maximize device efficiency: one molecule exhibiting thermally activated delayed fluorescence (TADF) and another molecule with a high fluorescence rate and narrow emission spectrum. The postulated role of a TADF sensitizer is to enable up-conversion of triplet to singlet excitons through the reverse intersystem crossing mechanism, which is followed by a Förster energy transfer to the fluorescent emitter. However, a second mechanism based on the direct triplet-to-singlet exciton transfer between TADF molecules is a priori possible, but its role in hyperfluorescence has not been investigated. Here we employ first-principles electronic structure and kinetic Monte Carlo simulations to study the hyperfluorescence mechanism in four pairs of TADF/fluorescent emitters. We demonstrate how the triplet-to-singlet energy transfer mechanism is, in some cases, the main driver for the quantum efficiency boost observed in hyperfluorescent devices.
The Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider the Importance of Solution Ions
Authors: Dratch Benjamin , Orozco-Gonzalez Yoelvis , Gadda Giovanni , Gozem Samer
Published: February 2022

Ionizable residues and monoatomic ions in solution modulate enzyme catalysis and the structural stability of proteins; however, the delicate interplay between these short-range charges and long-range charges, and their contributions to the electrostatic environment in a protein active site, is currently not fully understood. The study presented here utilizes the FMN-dependent NADH:quinone oxidoreductase from Pseudomonas aeruginosa PAO1 (NQO, EC 1.6.5.9, UniProtKB Q9I4V0) as a model system to study the effect of introducing an active site negative charge on the flavin absorption spectrum both in the absence and presence of a long-range electrostatic potential coming from solution ions. Using pH-dependent UV-visible spectroscopy, there were no observed changes in the flavin absorption spectrum when an active site tyrosine (Y277) deprotonated in vitro. These results could only be reproduced computationally using Average Solvent Electrostatic Configuration (ASEC) hybrid quantum mechanics / molecular mechanics (QM/MM) simulations that included both positive and negative solution ions. The same calculations performed with minimal ions to neutralize protein charges predicted that deprotonating Y277 would significantly affect the flavin absorption spectrum. Analyzing the distribution of solution ions from ASEC and radial distribution functions derived from molecular dynamics indicated that the solution ions reorganize around the protein surface upon Y277 deprotonation to cancel the effect of the tyrosinate on the flavin absorption spectrum. Biochemical experiments were performed to support this hypothesis. This work highlights the importance of salt ions, which are sometimes overlooked, since they can contribute a non-uniform and anisotropic long-range potential to the electrostatic environment of an active site.
Cheminformatics analysis of molecular datasets of transcription factors associated with quorum sensing in Pseudomonas aeruginosa
Authors: Victoria-Muñoz Felipe , Sánchez-Cruz Norberto , Medina-Franco José L. , López-Vallejo Fabian
Published: February 2022

Transcription factors associated with quorum sensing in P. aeruginosa are promising targets for developing new adjuvants against infection by this pathogen. Regulation of these transcription factors offers the possibility of controlling multiple virulence factors related to them, as the development of biofilm, proteases, hydrogen cyanide, and others. Numerous molecules have been tested against those targets, but the keys responsible for antagonistic activity against these targets are unknown. In this work, we analyze the structure-activity relationships of active molecules tested against LasR, PqsR, and RhlR transcription factors to establish the structural characteristics associated. The compounds were classified as agonist, antagonist, and inactive. As part of the analysis, we conducted molecular complexity, scaffold analyses, activity cliffs analyses, and chemical space visualization to find characteristics associated with the biological activity. Several structural features were identified as important to antagonist activity in this study, highlighting molecular size and hydrogen bond acceptors.
On the Role of the Electron-Dipole Interaction in Photodetachment Angular Distributions
Authors: Hart C. Annie , Lyle Justin , Spellberg Joseph , Krylov Anna I. , Mabbs Richard
Published: February 2022

The importance of including long-range electron-molecule interactions in treatments of photodetachment/photoionization is demonstrated. A combined experimental and computational study of CN− detachment is presented in which near threshold anisotropy parameters (β) are measured via photoelectron imaging. Calculated β values, based on an EOM-IP-CCSD/aug-cc-pVTZ Dyson orbital, are obtained using free particle and point dipole models. The results demonstrate the influence of the molecular dipole moment in the detachment process, and provide an explanation of the near threshold behavior of the overall photodetachment cross section in CN− detachment [J. Chem. Phys. 2020, 153, 184309]