bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural Product Scores and Fingerprints Extracted from Artificial Neural Networks.
Authors: Menke Janosch , Massa Joana , Koch Oliver
Published: February 2022

Due to their desirable properties, natural products are an important ligand class for medicinal chemists. However, due to their structural distinctiveness, traditional cheminformatic approaches, like ligand-based virtual screening, often perform worse for natural products. Based on our recent work, we evaluated the ability of neural networks to generate fingerprints more appropriate for use with natural products. A manually curated dataset of natural products and synthetic decoys was used to train a multilayer perceptron network and an autoencoder-like network. In-depth analysis showed that the extracted natural product-specific neural fingerprint outperforms traditional as well as natural product-specific fingerprints on three datasets. Further, we explored how the activations from the output layer of a network can work as a novel natural product likeness score. Overall, two natural product-specific datasets were generated, which are publicly available together with the code to create the fingerprints and the novel natural product likeness score.
Controlled self-assembly of modified aromatic amino acids
Authors: Gour Nidhi , Kshtriya Vivekshinh , Koshti Bharti , Narode Hanuman , Naskar Soumick
Published: February 2022

We report the self-assembly of carbobenzoxyphenylalanine (Z-Phe-OH), carbobenzoxytryptophan (Z-Trp-OH), carbobenzoxytyrosine (Z-Tyr-OH) and N-(9-Fluorenylmethoxycarbonyl)-O-tert-butyl-L-tyrosine (Fmoc-Tyr(tbu)-OH) to well-defined morphologies such as fibers, spherical and flower-like self-assembled structure. The self-assembled structure formed by modify single amino acids were characterized through various microscopic and spectroscopic techniques. The self-assembled structure formation was studied extensively under varying concentrations and temperature and the mechanism of self-assembled structure formation was extensively studied through solution state 1H NMR. The self-assembly studies on modified amino acid provide an important avenue for the simple fabrication and design of novel materials with immense applications. Hence, Z-Phe-OH, Z-Trp-OH, Z-Tyr-OH, and Fmoc-Tyr(tbu)-OH self-assembly studies may be a pertinent extension in this direction.
G-quadruplex inducer/stabilizer pyridostatin targets SUB1 to promote cytotoxicity of a transplatinum complex
Authors: Hou Yinzhu , Gan Tieliang , Fang Tiantian , Zhao Yao , Luo Qun , Liu Xingkai , Qi Luyu , Zhang Yanyan , Jia Feifei , Han Juanjuan , Li Shumu , Wang Shijun , Wang Fuyi
Published: February 2022

Pyridostatin (PDS) is a well-known G-quadruplex (G4) inducer and stabilizer, yet its target genes have remained unclear. Herein, combining mass spectrometry based proteomics strategy with bioinformatics analysis, we revealed that PDS significantly downregulated 22 proteins, of which the genes contain rich G4 potential sequences, in HeLa cancer cells, consequently upregulating 16 proteins remarkably. The PDS-regulated proteins appeared to work synergistically to activate cyclin and cell cycle regulation, and to restrain the inhibition of ARE-mediated mRNA decay pathway, suggesting that PDS itself is not a potential anticancer agent, at least towards HeLa cancer. Importantly, among the PDS targeted genes, SUB1, which expresses the human positive cofactor and DNA lesion sensor PC4, was down-regulated by 4.76-fold. Further studies demonstrated that the downregulation of PC4 dramatically promoted the cytotoxicity of trans-[PtCl2(NH3)(thiazole)] towards HeLa cells to a similar level to that of cisplatin, contributable to retarding the repair of 1,3-trans-platinated DNA lesion mediated by PC4. These findings not only provide new insights into better understanding on the biological functions of PDS, but also implicate a strategy for the rational design of novel multi-targeting platinum anticancer drugs via conjugation of PDS as a ligand to the coordination scaffold of transplatin for battling drug resistance to cisplatin.
Nickel-Catalyzed Intermolecular Alkyne Hydrohydrazonation
Authors: Wang Jian , Liu Junfeng , Manan Rajith , Ugrinov Angel , Kim Taehyun , Pan Yanxiong , Yang Zhongyu , Zhao Pinjing
Published: February 2022

We report a method for mild and atom-efficient synthesis of ketazines via nickel-catalyzed intermolecular hydroamination of internal alkynes with NH2-hydrazones. This alkyne hydrohydrazonation process is promoted by [Ni(cod)2] as a Ni(0) precatalyst and IPr as a N-heterocyclic carbene (NHC) ligand. A stoichiometric reaction between in situ generated [Ni(IPr)2] and benzophenone hydrazone (Ph2C=NNH2) led to the isolation of IPr-coordinated and hydroxo-bridged dinuclear Ni(II) hydrazonato complex [(IPr)Ni(HNN=CPh2)(miu2-OH)]2 that displayed high activity as a hydrohydrazonation pre-catalyst. We propose a catalytic cycle involving C-N bond formation via alkyne insertion into the Ni-N linkage of Ni(II) hydrazonato intermediates.
An Electrochemical Ethylamine/Acetonitrile Redox Method for Ambient Hydrogen Storage
Authors: Wu Dezhen , Li Jialu , Yao Libo , Xie Rongxuan , Peng Zhenmeng
Published: February 2022

Hydrogen storage presents a major difficulty in the development of hydrogen economy. Herein, we report a new electrochemical ethylamine/acetonitrile redox method for hydrogen storage with an 8.9 wt.% theoretical storage capacity under ambient conditions. This method exhibits low onset overpotentials of 0.19 V in CH3CH2NH2 dehydrogenation to CH3CN and 0.09 V in CH3CN hydrogenation to CH3CH2NH2 using commercial Pt black catalyst. By assembling a full cell that couples CH3CH2NH2/CH3CN redox reactions with hydrogen evolution and oxidation reactions, we demonstrate a complete hydrogen storage cycle at fast rates, with only 52.5 kJ/mol energy consumption for H2 uptake and release at a rate of 1 L/m2·h. This method provides a viable hydrogen storage strategy that meets the 2025 Department of Energy onboard hydrogen storage target.
Diversifying databases of metal organic frameworks for high-throughput computational screening
Authors: Majumdar Sauradeep , Moosavi Seyed Mohamad , Jablonka Kevin Maik , Ongari Daniele , Smit Berend
Published: February 2022

By combining metal nodes and organic linkers, an infinite number of metal organic frameworks (MOFs) can be designed in silico. When making new databases of such hypothetical MOFs, we need to assure that they not only contribute towards the growth of the count of structures but also add different chemistry to existing databases. In this study, we designed a database of ~20,000 hypothetical MOFs which are diverse in terms of their chemical design space—metal nodes, organic linkers, functional groups and pore geometries. Using Machine Learning techniques, we visualized and quantified the diversity of these structures. We find that on adding the structures of our database, the overall diversity metrics of hypothetical databases improve, especially in terms of the chemistry of metal nodes. We then assessed the usefulness of diverse structures by evaluating their performance, using grand-canonical Monte Carlo simulations, in two important environmental applications—post combustion carbon capture and hydrogen storage. We find that many of these structures perform better than widely used benchmark materials such as Zeolite-13X (for post combustion carbon capture) and MOF-5 (for hydrogen storage).
Synthesis of α- and β-Carbolines by a Metalation/Negishi Cross-Coupling/SNAr Reaction Sequence
Authors: Roesner Stefan , Sathiyalingam Shainthavaan
Published: February 2022

Carbolines are privileged scaffolds in medicinal chemistry, and therefore, novel and efficient approaches to their synthesis are in high demand. An efficient method for the synthesis of α- and β-carbolines from fluoropyridines and 2-haloanilines is reported. This streamlined procedure consists of a four-step directed ortho-lithiation, zincation, Negishi cross-coupling, and intramolecular nucleophilic aromatic substitution, providing access to a diverse set of functionalised carbolines. While the procedure is applicable to batch conditions, the generation of arylzinc intermediates in continuous flow has been demonstrated .
PNA Microprobe for Label-Free Detection of Nucleic Acid Repeat Mutations
Authors: Shamsi Mohtashim , Asefifeyzabadi Narges , Durocher Grace , Tshilenge Kizito-Tshitoko , Ellerby Lisa
Published: February 2022

We present a PNA-based microprobe sensing platform to detect nucleic acid repeat mutations by electrochemical impedance spectroscopy. The microprobe platform discriminated Huntington’s disease-associated CAG repeats in cell-derived total RNA. This sensitive, label-free, and PCR-free detection strategy has the potential to detect a plethora of length mutation disorders.
How Radical are ‘Radical’ Photocatalysts? A Closed-Shell Meisenheimer Complex is Identified as a Super-reducing Photoreagent
Authors: Rieth Adam , Gonzalez Miguel , Kudisch Bryan , Nava Matthew , Nocera Daniel
Published: February 2022

Super-reducing excited states have the potential to activate strong bonds, leading to unprecedented photoreactivity. Excited states of radical anions, accessed via reduction of a precatalyst followed by light absorption, have been proposed to drive photoredox transformations under super-reducing conditions. Here we investigate the radical anion of naphthalene monoimide as a photoreductant and find that the radical doublet excited state has a lifetime of 24 ps, which is too short to facilitate photoredox activity. To account for the apparent photoreactivity of the radical anion, we identify an emissive two-electron reduced Meisenheimer complex of naphthalene monoimide, [NMI(H)]–. The singlet excited state of [NMI(H)]– is a potent reductant (–3.08 V vs Fc/Fc+), is long-lived (20 ns), and its emission can be dynamically quenched by chloroarenes to drive a radical photochemistry, establishing that it is this emissive excited state that is competent for reported C–C and C–P coupling reactivity. These results provide a mechanistic basis for photoreactivity at highly reducing potentials via singlet excited state manifolds and lays out a clear path for the development of exceptionally reducing photoreagents derived from electron-rich closed-shell anions.
Comparing Two Seized Drug Workflows for the Analysis of Synthetic Cannabinoids, Cathinones, and Opioids
Authors: Sisco Edward , Burns Amber , Schneider Elizabeth , Miller IV Charles R. , Bobka Laurel
Published: February 2022

As the challenges faced by drug chemists continue to persist due to the presence of synthetic opioids, novel psychoactive substances, and other emerging drugs, laboratories are continuing to look for new analytical approaches or techniques to ease the burdens. These new solutions can range from simple changes in existing methods to better distinguish isomers to adoption and implementation of entirely new technologies for screening or confirmation. One barrier to making these transitions is lack of data to understand how, or even if, workflow changes will address the challenges. In this study, we attempt to compare, qualitatively and quantitatively, an existing analytical workflow for seized drug analysis to a new, experimental workflow to better understand the potential benefits and drawbacks. Using adjudicated and mock case samples containing synthetic cannabinoids, synthetic cathinones, and opioids, four forensic chemists were asked to analyze fifty samples using one of two workflows. The first was an existing workflow that employed color tests for screening alongside general purpose gas chromatography flame ionization detection (GC-FID) and general purpose gas chromatography mass spectrometry (GC-MS) analyses for confirmation. The second was an experimental workflow that combined direct analysis in real time mass spectrometry (DART-MS) for screening with class-specific (targeted) GC-MS methods for confirmation. At each step in the analysis scheme, chemists recorded the time required and as well as their interpretation of the results. Comparison of the workflows showed that screening by DART-MS required the same amount of time as color tests but yielded significantly more accurate, and specific, information. Confirmation using the general purpose GC-FID and GC-MS methods of the existing workflow required more than twice the amount of instrument time and data interpretation time while also presenting other analytical challenges that prevented compound confirmation in select samples. Use of targeted GC-MS methods simplified data interpretation, reduced consumption of reference materials, and addressed almost all the limitations of general purpose methods. While the experimental workflow is not yet validated for casework, this study shows how rethinking analytical workflows for seized drug analysis could greatly assist laboratories in reducing turnaround times, backlogs, and standards consumption. It also demonstrates the potential impact of being able to investigate workflow changes prior to implementation.
Ruffling is Essential for Staphylococcus aureus IsdG-catalyzed Degradation of Heme to Staphylobilin
Authors: Schuelke-Sanchez Ariel , Cornetta Amanda , Kocian Taylor , Conger Matthew , Liptak Matthew
Published: February 2022

Non-canonical heme oxygenases are enzymes that degrade heme to non-biliverdin products within bacterial heme iron acquisition pathways. These enzymes all contain a conserved second-sphere Trp residue that is essential for enzymatic turnover. Previous studies have revealed several important roles for the conserved second-sphere Trp in Staphylococcus aureus IsdG, S. aureus IsdI, and Mycobacterium tuberculosis MhuD. However, a general model for the geometric, electron-ic, and functional role of the second-sphere Trp had not been deduced prior to this work. Here, UV/Vis absorption (Abs) and circular dichroism (CD) spectroscopies were employed to show that the W67F variant of IsdG perturbs the heme substrate conformation without altering the protein secondary structure. In general, it can now be stated that a dynamic equilibrium between “planar” and “ruffled” substrate conformations exists within non-canonical heme oxygenases, and that the second-sphere Trp favors population of the “ruffled” substrate conformation. 1H nuclear magnetic resonance and magnetic CD spectroscopies were used to characterize the electronic structures of IsdG and IsdI variants with different substrate conformational distributions. These data revealed that the “ruffled” substrate conformation promotes partial porphyrin-to-iron electron transfer, which makes the meso carbons of the porphyrin ring susceptible to radical attack. Finally, UV/Vis Abs spectroscopy was utilized to quantify the enzymatic rates, and electrospray ionization mass spec-trometry was used to identify the product distributions, for variants of IsdG with altered substrate conformational distri-butions. In general, the rate of heme monooxygenation to meso-hydroxyheme by non-canonical heme oxygenasess de-pends upon the population of the “ruffled” substrate conformation. Also, the production of staphylobilin or mycobilin by these enzymes is correlated with the population of the “ruffled” substrate conformation, since variants that favor popula-tion of the “planar” substrate conformation yield significant amounts of biliverdin. These data can be understood within the framework of a concerted rearrangement mechanism for the monooxygenation of heme to meso-hydroxyheme by non-canonical heme oxygenases. However, the mechanisms of IsdG/IsdI and MhuD must diverge following this interme-diate in order to generate distinct staphylobilin and mycobilin products, respectively.
Ruffling is Essential for Staphylococcus aureus IsdG-catalyzed Degradation of Heme to Staphylobilin
Authors: Schuelke-Sanchez Ariel , Cornetta Amanda , Kocian Taylor , Conger Matthew , Liptak Matthew
Published: February 2022

Non-canonical heme oxygenases are enzymes that degrade heme to non-biliverdin products within bacterial heme iron acquisition pathways. These enzymes all contain a conserved second-sphere Trp residue that is essential for enzymatic turnover. Previous studies have revealed several important roles for the conserved second-sphere Trp in Staphylococcus aureus IsdG, S. aureus IsdI, and Mycobacterium tuberculosis MhuD. However, a general model for the geometric, electronic, and functional role of the second-sphere Trp had not been deduced prior to this work. Here, UV/Vis absorption (Abs) and circular dichroism (CD) spectroscopies were employed to show that the W67F variant of IsdG perturbs the heme substrate conformation without altering the protein secondary structure. In general, it can now be stated that a dynamic equilibrium between “planar” and “ruffled” substrate conformations exists within non-canonical heme oxygenases, and that the second-sphere Trp favors population of the “ruffled” substrate conformation. 1H nuclear magnetic resonance and magnetic CD spectroscopies were used to characterize the electronic structures of IsdG and IsdI variants with different substrate conformational distributions. These data revealed that the “ruffled” substrate conformation promotes partial porphyrin-to-iron electron transfer, which makes the meso carbons of the porphyrin ring susceptible to radical attack. Finally, UV/Vis Abs spectroscopy was utilized to quantify the enzymatic rates, and electrospray ionization mass spectrometry was used to identify the product distributions, for variants of IsdG with altered substrate conformational distributions. In general, the rate of heme oxygenation by non-canonical heme oxygenases depends upon the population of the “ruffled” substrate conformation. Also, the production of staphylobilin or mycobilin by these enzymes is correlated with the population of the “ruffled” substrate conformation, since variants that favor population of the “planar” substrate conformation yield significant amounts of biliverdin. These data can be understood within the framework of a concerted rearrangement mechanism for the monooxygenation of heme to meso-hydroxyheme by non-canonical heme oxygenases. However, the mechanisms of IsdG/IsdI and MhuD must diverge following this intermediate in order to generate distinct staphylobilin and mycobilin products, respectively.
Fast Reverse Intersystem Crossing Over 107 s-1 in Organic Emitters with Inverted Singlet-Triplet Gap via Intramolecular Through Space Charge Transfer
Authors: Wang Yafei , Chen Xinrui , Pollice Robert , Li Bing , Zhu Yuanyuan , Lv Anqi , Liu Yuchao , Ren Zhongjie , Ma Huili , Zhu Weiguo , Aspuru-Guzik Alán
Published: February 2022

Controlling excited state properties to achieve fast reverse intersystem crossing rates of over 107 s-1 is still challenging for intramolecular through-space charge transfer (TSCT) based delayed fluorescent materials. To gain further insight into the relationship between through-space and through-bond charge transfer (TSCT/TBCT), herein, three compounds DPS-24Ac, DPS-25Ac and DPS-OAc were prepared and characterized via NMR, MS and single crystal, in which the diphenylsulfone (DPS) is used as the acceptor group and acridine (Ac) as the donor moiety. Intense emissions from blue to yellow with high emission efficiency of 70-100% are detected for all emitters. Both computations and experiments suggest that compounds DPS-24Ac and DPS-25Ac have a clear TSCT effect and also an inverted adiabatic singlet-triplet gap which can be explained by the kinetic exchange mechanism. Notably, compound DPS-24Ac achieves the highest reverse intersystem crossing rate constant (krISC) of over 107 s-1 via manipulation of both TSCT and TBCT effects. The solution-processed devices display maximum external quantum efficiencies of 21.73, 12.14 and 4.96% for DPS-24Ac, DPS-25Ac and DPS-OAc, respectively. Overall, this work provides a novel avenue to achieve highly-efficient OLED materials with fast rISC by controlling both TSCT and TBCT effects.
Olefin-surface interactions: a key activity parameter in silica-supported olefin metathesis catalysts
Authors: Berkson Zachariah , Bernhardt Moritz , Schlapansky Simon , Benedikter Mathis , Buchmeiser Michael , Price Gregory , Sunley Glenn , Copéret Christophe
Published: February 2022

Molecularly defined and classical heterogenous Mo-based metathesis catalysts are shown to display dis-tinct and unexpected reactivity patterns for the metathesis of long-chain α-olefins at low temperatures (< 100 °C). Namely, catalysts based on supported Mo oxo species, whether prepared via wet impregnation or surface organometallic chemistry (SOMC), exhibit strong activity dependencies on the α-olefin chain length, with slower reaction rates for longer substrate chain lengths. In contrast, molecular and support-ed Mo alkylidenes are highly active and do not display such dramatic dependence on chain length. State-of-the-art 2D solid-state NMR analyses of post-metathesis catalysts, complemented by FTIR and molecular dynamics calculations, evidence that the activity decrease observed for supported Mo oxo catalysts relates to the strong adsorption of internal olefin metathesis products due to interactions with surface Si-OH groups. Overall, this study shows that in addition to the nature and the number of active sites, the metathesis rates and overall catalytic performance depend on product desorption, even in the liquid phase with non-polar substrates. This study further highlights the role of support and active site composition and dynamics on activity as well as the need to consider adsorption in catalyst design.
MB-Fit: Software Infrastructure for Data-Driven Many-Body Potential Energy Functions
Authors: Bull-Vulpe Ethan , Riera Marc , Goetz Andreas , Paesani Francesco
Published: February 2022

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions, from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the auto- mated development of MB-PEFs for generic molecules within the TTM-nrg (“Thole-type model energy”) and MB-nrg (“many-body energy”) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy/force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, we believe that MB-Fit will enable routine, predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.
Machine-Learned Energy Functionals for Strongly Correlated Systems
Authors: King Daniel , Gagliardi Laura , Truhlar Donald
Published: February 2022

We introduce multiconfiguration data-driven functional theory (MC-DDFT) as a new approach to multiconfiguration nonclassical functional theory (MC-NCFT), in which the classical energy of a multiconfigurational wave function is combined with a machine-learned functional for the nonclassical exchange-correlation energy. We also present results obtained by a related approach, multiconfiguration energy-correcting functional theory (MC-ECFT), in which the total energy of a wave function method (e.g. CASSCF or NEVPT2) is corrected with a machine-learned functional. On a dataset of carbene singlet-triplet energy splittings, we demonstrate that these new multiconfiguration data-driven functional methods (MC-DDFMs) are able to achieve near-benchmark performance on systems not used for training while being less active-space dependent than multiconfiguration pair-density functional theory using currently available translated functionals.
Radiative Contributions Dominate Plasmon Broadening for Post-Transition Metals in the Ultraviolet
Authors: Fonseca Guzman Maria , Ross Michael
Published: February 2022

We use classical electrodynamics calculations to investigate the plasmonic properties of the post-transition metals Al, Bi, Ga, In, and Sn, which are active in the ultraviolet, focusing in particular on the material- and resonance-dependent origins of plasmon broadening. Analytic Mie theory, the modified-long wavelength approximation, and the quasistatic dipole approximation together show that radiative processes dominate plasmon dephasing and damping in small (5–25 nm radius) Al, Bi, Ga, In, and Sn spheres. For Al, Ga, In, and Sn, the radiative contribution (~0.1–0.2 eV) to the plasmon linewidth is 100-fold greater than the non-radiative contribution (0.001–0.02 eV) derived from the bulk dielectric function. This is significantly different than what is observed for Ag spheres, where non-radiative contributions (~0.1 eV) are the primary source of broadening up to a radius of 25 nm. Overall, these data suggest that the plasmonic properties, dephasing, and lifetimes for Al, Ga, In, and Sn —and to a lesser extent Bi— spheres are qualitatively similar. To develop a more general understanding of the relationship between plasmon energy and linewidth, we use a model for ideal free-electron Drude metals. It is seen that the linewidth increases at higher energies even for lossless Drude metals, suggesting that the increased broadening observed in UV-active metals is a generalizable observation. These data have important implications for the use of these metals for ultraviolet plasmonics. The increased importance of radiative damping for post-transition metals could influence the ability to harvest photons, generate hot carriers, and enhance spectroscopy in the ultraviolet while providing new opportunities for manipulating high-energy photons.
A Free Aluminylene with Diverse σ-Donating and Doubly σ/π-Accepting Ligand Features for Transition Metals
Authors: Zhang Xin , Liu Liu Leo
Published: February 2022

Aluminium based ligands have garnered tremendous interest in the past decades due to the fundamental significance of the structural and electronic properties as well as their applications in synthetic chemistry. We report herein the synthesis, characterization, and coordination chemistry of a free N-aluminylene, namely a carbazolylaluminylene 2b. This species is prepared via a reduction reaction of the corresponding carbazolyl aluminium diiodide and is stable under an inert atmosphere. The coordination behavior of 2b towards transition metal centers (Mn, W, Cr) is shown to afford a series of novel aluminylene complexes with diverse coordination modes. We demonstrate that the Al center in 2b can behave as: 1. a σ-donating and doubly π-accepting ligand; 2. a σ-donating, σ-accepting and π-accepting ligand; and 3. σ-donating and doubly σ-accepting ligand. Additionally, we show ligand exchange at the aluminylene center providing access to the modulation of electronic properties of transition metals without changing the coordinated atoms. Further investigations of 2b with IDippCuCl (IDipp = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) showcase an unprecedented one-step aluminylene-alumanyl transformation leading to the facile synthesis of a rare terminal Cu-alumanyl complex. The electronic structures of such complexes and the mechanism of the unusual aluminylene-alumanyl transformation are investigated through density functional theory (DFT) calculations.
A Free Aluminylene with Diverse σ-Donating and Doubly σ/π-Accepting Ligand Features for Transition Metals
Authors: Zhang Xin , Liu Liu Leo
Published: February 2022

We report herein the synthesis, characterization, and coordination chemistry of a free N-aluminylene, namely a carbazolylaluminylene 2b. This species is prepared via a reduction reaction of the corresponding carbazolyl aluminium diiodide. The coordination behavior of 2b towards transition metal centers (W, Cr) is shown to afford a series of novel aluminylene complexes 3-6 with diverse coordination modes. We demonstrate that the Al center in 2b can behave as: 1. a σ-donating and doubly π-accepting ligand; 2. a σ-donating, σ-accepting and π-accepting ligand; and 3. a σ-donating and doubly σ-accepting ligand. Additionally, we show ligand exchange at the aluminylene center providing access to the modulation of electronic properties of transition metals without changing the coordinated atoms. Investigations of 2b with IDippCuCl (IDipp = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) show an unprecedented aluminylene-alumanyl transformation leading to a rare terminal Cu-alumanyl complex 8. The electronic structures of such complexes and the mechanism of the aluminylene-alumanyl transformation are investigated through density functional theory (DFT) calculations.
Flexible boundary layer using exchange for embedding theories. I. Theory and implementation
Authors: Shen Zhuofan , Glover William
Published: February 2022

Embedding theory is a powerful computational chemistry approach to exploring the electronic structure and dynamics of complex systems, with QM/MM being the prime example. A challenge arises when trying to apply embedding methodology to systems with diffusible particles, e.g. solvents, if some of them must be included in the QM region, for example in the description of solvent-supported electronic states or reactions involving proton transfer or charge-transfer-to-solvent: without a special treatment, inter-diffusion of QM and MM particles will lead eventually to a loss of QM/MM separation. We have developed a new method called Flexible Boundary Layer using Exchange (FlexiBLE) that solves the problem by adding a biasing potential to the system that closely maintains QM/MM separation. The method rigorously preserves ensemble averages by leveraging their invariance to exchange of identical particles. With a careful choice of the biasing potential, and the use of a tree algorithm to include only important QM and MM exchanges, we find the method has an MM-forcefield-like computational cost and thus adds negligible overhead to a QM/MM simulation. Furthermore, we show that molecular dynamics with the FlexiBLE bias conserves total energy and remarkably, dynamical quantities in the QM region are unaffected by the applied bias. FlexiBLE thus widens the range of chemistry that can be studied with embedding theory.
C-H Oxidation in Fluorenyl Benzoates Does Not Proceed Through a Stepwise Pathway: Revisiting Asynchronous Proton-Coupled Electron Transfer
Authors: Coste Scott , Brezny Anna , Koronkiewicz Brian , Mayer James
Published: February 2022

2-fluorenyl benzoates were recently shown to undergo C–H bond oxidation through intramolecular proton transfer coupled with electron transfer to an external oxidant. Kinetic analysis revealed unusual rate-driving force relationships and indicated a mechanism of multi-site concerted proton-electron transfer (MS-CPET) for all reactions. More recently, an alternative interpretation of the data was proposed to explain the rate-driving force relationships, invoking a crossover from CPET to a stepwise mechanism with an initial intramolecular proton transfer (PT) (Costentin, Savéant, Chem. Sci., 2020, 11, 1006). Here, we show that this proposed alternative pathway is untenable based on new experimental assessments of the intramolecular PT equilibrium constant and rates. Measurement of the fluorenyl 9-C–H pKa, H/D exchange experiments, and kinetic modelling eliminate the possibility of a stepwise mechanism for C–H oxidation in the fluorenyl benzoate series. Implications for asynchronous MS-CPET mechanisms are discussed with respect to classical Marcus theory and the quantum-mechanical treatment of CPET.
Sterically Stabilized End-On Superoxocopper(II) Complexes and Mechanistic Insights Into Their Reactivity With O-H, N-H and C-H Substrates.
Authors: Quek Sebastian , Debnath Suman , Laxmi Shoba , van Gastel Maurice , England Jason
Published: February 2022

Instability of end-on superoxocopper(II) complexes, with respect to conversion to the corresponding peroxo-bridged complexes, has largely constrained their study to very low temperatures (< -80°C). This limits their kinetic capacity to oxidize substrates. In response, we have developed a series of ligand systems bearing bulky aryl substituents that are primarily directed away from the metal centre, Ar3-TMPA (Ar = tpb, dpb, dtbpb), and used them to support [Cu(Ar3-TMPA)(NCMe)]+ copper(I) complexes. Solutions of all three react with O2 to yield [Cu(η1-O2•−)(Ar3-TMPA)]+ complexes that are stable against dimerization at all temperatures. Full binding of O2 is observed at sub-ambient temperatures and can be reversed by warming. The onset of oxygenation is ligand dependent, but can be observed at 25°C in the case of Ar = tpb and dpb. Furthermore, all three [Cu(η1-O2•−)(Ar3-TMPA)]+ complexes are stable against self-decay at temperatures ≤ -20°C. This provides a wide temperature window over which these complexes can be studied, which was exploited by performing extensive reaction kinetics measurements for [Cu(η1-O2•−)(tpb3-TMPA)]+ with a broad range of O-H, N-H, and C-H bond substrates. This includes correlation of second order rate constants (k2 values) versus oxidation potentials (Eox) for a range of phenols (i.e., a Marcus plot), construction of Eyring plots, and temperature-dependent kinetic isotope effect (KIE) measurements. The data obtained indicates that reaction with all substrates proceeds via H-atom transfer (HAT) to [Cu(η1-O2•−)(tpb3-TMPA)]+. In addition, evidence suggests that HAT reaction with the phenols studied proceeds with significant charge transfer, and that it involves full tunelling of both H and D atoms in the case of 1,2-diphenylhydrazine (DPH) and 4-methoxy-2,6-di-tert-butylphenol (MeO-ArOH). Consistent with expectations for HAT, large entropic barriers (ΔS‡) were measured for the substrates MeO-ArOH, DPH, triphenylhydrazine (TPH), and 1-benzyl-1,4-dihydronicotinamide (BNAH). Despite having the lowest X-H bond dissociation energy (BDE) amongst these substrates, the C-H substrate BNAH exhibits both the largest ΔS‡ and the second largest enthalpic barrier (ΔH‡) to reaction. This is congruent with the expectation that oxidation of C-H bonds is kinetically challenging and the experimental observation that [Cu(η1-O2•−)(tpb3-TMPA)]+ is only able to oxidize very weak C-H bonds, whereas it can oxidize moderately strong N-H bonds.
Nitrene Photochemistry of Manganese N-Haloamides
Authors: Van Trieste Gerard , Hicks Madeline , Das Anuvab , Bhuvanesh Nattamai , Ozarowski Andrew , Telser Joshua , Powers David
Published: February 2022

Here we report the synthesis and nitrene transfer photochemistry of Mn(III) N-haloamide complexes. Photolysis results in both C–H bond amination and olefinic aziridination products. Low-temperature spectroscopy indicates halogen-dependent photoreactivity: Photolysis of N-chloroamides cleaves the Mn–N bond to generate Mn(II) and amidyl radical species; in contrast, photolysis of N-iodoamides proceeds via N–I cleavage yielding a formally Mn(IV) nitrenoid.
Ultrafast Proton Transfer Reaction in Phenol–(Ammonia)n Clusters: An Ab-Initio Molecular Dynamics Investigation.
Authors: Singh Reman Kumar , Pant Rakesh , Patwari G Naresh
Published: February 2022

The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer process, the phenol molecule must be embedded in a cluster consisting of at least eight ammonia molecules, even though several local minima with proton transferred can be observed for clusters consisting of 5-7 ammonia molecules. Further, phenol solvated in large clusters of ammonia, the proton transfer is spontaneous with the proton transfer event being instantaneous (about 20-120 fs). These simulations indicate that the rate-determining step for the proton transfer process is the reorganization of the solvent around the OH group and the proton transfer process in phenol-(ammonia)n clusters. The fluctuations in the solvent occur until a particular set of configurations projects the field in excess of critical electric field along the O–H bond which drives the proton transfer process with a respone time of about 70 fs. Further, the proton transfer process follows a curvilinear path which includes the O–H bond elongation and out-of-plane movement of the proton and can be referred to as a “Bend-to-Break” process.
Evaluating Fast Methods for Static Polarizabilities on Extended Conjugated Oligomers
Authors: Heiner Danielle , Folmsbee Dakota , Langkamp Luke , Hutchison Geoffrey
Published: February 2022

Given the importance of accurate polarizability calculations to many chemical applications, coupled with the need for efficiency when calculating the properties of sets of molecules or large oligomers, we present a benchmark study examining possible calculation methods for polarizable materials. We first investigate the accuracy of highly-efficient semi-empirical tight-binding method GFN2-xTB, and the popular D4 dispersion model, comparing its predicted additive polarizabilities to ωB97X-D results for a subset of PubChemQC and a compiled benchmark set of molecules spanning polarizabilities from approximately 3-600 Å^3, with a few compounds in the range of approximately 1200-1400 Å^3. Although we find GFN2 to have large errors with polarizability calculations, on large oligomers it would appear a quadratic correction factor can remedy this. We also compare the accuracy of DFT polarizability calculations run using basis sets of varying size and level of augmentation, determining that a non-augmented basis set may be used for highly polarizable species in conjunction with a linear correction factor to achieve accuracy extremely close to that of aug-cc-pVTZ.
Dimethoxytriazine-Triazole Linked Mesoporous Silica Hybrid Sorbent for Cationic Dyes Adsorption
Authors: Saad Ali , Jlassi Khouloud , Abderrabba Manef , CHEHIMI Mohamed
Published: February 2022

Organic dye has always been considered one of the most serious water pollutants. Therefore, the great significance nowadays is to synthesis effective adsorbent Materials for removal of these contaminants. Herein, we prepared successfully a novel sorbent based on dimethoxy-triazine/triazole groups functionalized via a 1,3-dipolar cycloaddition click reaction on mesoporous silica SBA-15. The resulting sample denoted DMT-Tr-SBA-15 was characterized by FTIR spectra, X-ray photoelectron spectroscopy (XPS), solid-state 13C NMR spectroscopy and nitrogen adsorption/desorption isotherm. The resulting hybrid silica material was evaluated as a sorbent for adsorption of four cationic dyes in aqueous media showed high adsorption efficiency and a fast removal rate. The adsorption properties were monitored versus time; the after 40 min and using a 40 mg/L of adsorbent was reached. The maximum adsorption capacity for methylene blue at room temperature and neutral pH was 4.59 mmol g-1. These results indicate the great potential of clickable mesoporous silica to diversify the active sites for adsorption, thus demonstrating a significant interest for environmental applications.
Optoelectronic and elastic response of fluorinated hexagonal boron nitride monolayer
Authors: Bhandari Sharma Shambhu
Published: February 2022

The inherited insulating behavior of hexagonal boron nitride (h-BN) monolayer restricts its application in several optoelectronic devices, so finding a technique to reduce the bandgap allows it to possess the semiconducting functionality. Here, an experimentally feasible fluorinated hexagonal boron nitride (FBNF), a structurally, dynamically, and mechanically stable monolayer is reported by using density functional theory calculations. The significant geometrical transformation from planer h-BN to buckled FBNF softens the structure by retaining the mechanical isotropy and structural symmetry. Remarkably, the induced direct bandgap semiconducting behavior after fluorination enhances the optical absorbance and reflectivity reduces energy loss, creates strong optical anisotropy, and makes FBNF monolayer is a proper material in the optoelectronic and nanomechanical applications
Spontaneous and Ion-Specific Formation of Inverted Bilayers at Air/Aqueous Interface
Authors: Nayak Srikanth , Kumal Raju R , Uysal Ahmet
Published: February 2022

Amphiphilic lipid-ion interactions at aqueous interfaces drive the assisted ion transport in various biological and industrial systems. In chemical separations of heavy elements, lipids coordinate metal ions and solubilize them in an organic phase. Direct observation of lipid-metal interactions is highly difficult at the buried oil/water interface, and is accessible with limited experiments. Here, we demonstrate that inverted bilayer structures previously observed at oil/aqueous interfaces can also be formed at the air/aqueous interface. This facilitates the easier study of lipid-ion interactions over a wide range of parameters with multiple probes, including synchrotron X-ray reflectivity (XR), X-ray fluorescence near total reflection (XFNTR), and vibrational sum-frequency generation spectroscopy (VSFG). The formation of bilayers is highly sensitive to the metal ion charge density. While Lu3+ (115 C/mm3) lead to bilayer formation, Nd3+ (82 C/mm3) and Sr2+ (33 C/mm3) lead to monolayers. By introducing Lu3+ ions to preformed lipid monolayers, we extract kinetic parameters corresponding to monolayer to inverted bilayer conversion. Temperature-dependent studies show Arrhenius behavior with an energy barrier of 40 kcal/mol. The kinetics of monolayer to inverted bilayer conversion is also affected by the presence of background salts where thiocyanate accelerates the conversion more than nitrate does. Our results show the outsized importance of ion-specific effects on interfacial structure and kinetics, pointing to their role in chemical separation methods. Finally, this model system can be used to study a wide variety of lipid-ion interactions, opening a new avenue in molecular-scale understanding of these important systems.
Spontaneous and Ion-Specific Formation of Inverted Bilayers at Air/Aqueous Interface
Authors: Nayak Srikanth , Kumal Raju R , Uysal Ahmet
Published: February 2022

Developing better separation technologies for rare earth metals is important for a sustainable economy. However, the chemical similarities between rare earths make their separations difficult. Identifying molecular scale interactions that amplify the subtle differences between the rare earths can be useful in developing new separation technologies. Here, we describe ion-dependent monolayer to inverted bilayer transformation of extractant molecules at the air/aqueous interface. The inverted bilayers form with Lu3+ ions but not with Nd3+. By introducing Lu3+ ions to preformed monolayers, we extract kinetic parameters corresponding to the monolayer to inverted bilayer conversion. Temperature-dependent studies show Arrhenius behavior with an energy barrier of 40 kcal/mol. The kinetics of monolayer to inverted bilayer conversion is also affected by the character of the background anion, although anions are expected to be repelled from the interface. Our results show the outsized importance of ion-specific effects on interfacial structure and kinetics, pointing to their role in chemical separation methods.
A mechanistic investigation of the Pd-catalyzed cross-coupling between N-tosylhydrazones and aryl halides
Authors: Thomas Gilian , Ronda Kiera , McIndoe Scott
Published: February 2022

The cross-coupling of N-tosylhydrazones and aryl halides forms carbon-carbon bonds, producing 1,1-disubstituted alkenes. Though it has proven extremely useful in several fields of chemistry, its mechanism remains experimentally unexplored. Combining benchtop NMR and real-time mass spectrometry afforded the ability to monitor the catalytic intermediates as well as the rate of product formation.
The Role of Areal Capacity in Determining Short Circuiting of Sulfide-Based Solid-State Batteries
Authors: Lewis John , Lee Chanhee , Liu Yuhgene , Han Sang Yun , Prakash Dhruv , Klein Emily , Lee Hyun-Wook , McDowell Matthew
Published: February 2022

Solid-state batteries (SSBs) with lithium metal anodes offer higher specific energy than conventional lithium-ion batteries, but they must utilize areal capacities >3 mAh cm-2 and cycle at current densities >3 mA cm-2 to achieve commercial viability. Substantial research effort has focused on increasing rate capabilities of SSBs by mitigating detrimental processes such as lithium filament penetration. Less attention has been paid to understanding how areal capacity impacts plating/stripping behavior, despite the importance of areal capacity for achieving high specific energy. Here, we investigate and quantify the relationships among areal capacity, current density, and plating/stripping stability using both symmetric and full-cell configurations with a sulfide solid-state electrolyte (Li6PS5Cl). We show that unstable deposition and short circuiting readily occur at rates much lower than the measured critical current density when a sufficient areal capacity is passed. A systematic study of continuous plating under different electrochemical conditions reveals average “threshold capacity” values at different current densities, beyond which short circuiting occurs. Cycling cells below this threshold capacity significantly enhances cell lifetime, enabling stable symmetric cell cycling at 2.2 mA cm-2 without short circuiting. Finally, we show that full cells also exhibit threshold capacity behavior, but they tend to short circuit at lower current densities and areal capacities. Our results quantify the effects of transferred capacity and demonstrate the importance of using realistic areal capacities in experiments to develop viable solid-state batteries.
Structure of the active pharmaceutical ingredient bismuth subsalicylate
Authors: Svensson Grape Erik , Rooth Victoria , Nero Mathias , Willhammar Tom , Inge A. Ken
Published: February 2022

Structure determination of pharmaceutical compounds is invaluable for drug development but is challenging for materials that form as small crystals with defects. Bismuth subsalicylate (BSS), among the most commercially significant bismuth compounds, is an active ingredient in over-the-counter medications such as Pepto-Bismol (genericized trademark), used to treat dyspepsia and H. pylori infections. Despite its century-long history, the structure has remained unknown. Three-dimensional electron diffraction and hierarchical clustering analysis were applied on select data from ordered crystals, revealing a layered structure. In less ordered crystals high-resolution scanning transmission electron microscopy revealed various disorders, including variations in the stacking of layers. These modern electron crystallography techniques provide insight into differences in BSS crystals and the possibility to develop new analogs or polymorphs.