bluuebunny/crossref_metadata_2025 huggingface dataset:
Microfluidic oxygen tolerability screening of nanocarriers for triplet fusion photon upconversion
Authors: Isokuortti Jussi , Kiiski Iiro , Sikanen Tiina , Durandin Nikita , Laaksonen Timo
Published: February 2022

The full potential of triplet fusion photon upconversion (TF-UC) of providing high-energy photons locally with low-energy excitation is limited in biomedicine and life sciences by its oxygen sensitivity. This hampers the applicability of TF-UC systems in sensors, imaging, optogenetics and drug release. Despite the advances in improving the oxygen tolerability of TF-UC systems, the evaluation of oxygen tolerability is based on comparing the performance at completely deoxygenated (0 % oxygen) and ambient (20–21 %) conditions, leaving the physiological oxygen levels (0.3–13.5 %) neglected. This oversight is not deliberate and is only the result of the lack of simple and predictable methods to obtain and maintain these physiological oxygen levels in an optical setup. Herein, we demonstrate the use of microfluidic chips made of oxygen depleting materials to study the oxygen tolerability of four different micellar nanocarriers made of FDA-approved materials with various oxygen scavenging capabilities by screening their TF-UC performance over physiological oxygen levels. All nanocarriers were capable of efficient TF-UC even in ambient conditions. However, utilizing oxygen scavengers in the oil phase of the nanocarrier improves the oxygen tolerability considerably. For example, at the mean tumour oxygen level (1.4 %), nanocarriers made of surfactants and oil phase both capable of oxygen scavenging retained remarkably 80 % of their TF-UC emission. This microfluidic concept enables faster, simpler and more realistic evaluation of, not only TF-UC, but any micro or nanoscale oxygen-sensitive system and facilitates their development and implementation in biomedical and life science applications.
Chemformer: A Pre-Trained Transformer for Computational Chemistry
Authors: Irwin Ross , Dimitriadis Spyridon , He Jiazhen , Bjerrum Esben
Published: February 2022

Transformer models coupled with Simplified Molecular Line Entry System (SMILES) have recently proven to be a powerful combination for solving challenges in cheminformatics. These models, however, are often developed specifically for a single application and can be very resource-intensive to train. In this work we present Chemformer model – a Transformerbased model which can be quickly applied to both sequence-to-sequence and discriminative cheminformatics tasks. Additionally, we show that self-supervised pre-training can improve performance and significantly speed up convergence on downstream tasks. On direct synthesis and retrosynthesis prediction benchmark datasets we publish state-of-the-art results for top- 1 accuracy. We also improve on existing approaches for a molecular optimisation task and show that Chemformer can optimise on multiple discriminative tasks simultaneously. Models, datasets and code will be made available after publication.
Assessing the importance of cation size in the tetragonal-cubic phase transition in lithium garnet electrolytes.
Authors: Stockham Mark , Griffiths Alice , Dong Bo , Slater Peter
Published: February 2022

Lithium garnets are promising solid-state electrolytes for next generation lithium-ion batteries. These materials have high ionic conductivity, a wide electrochemical window and stability with Li metal. However, lithium garnets have a maximum limit of 7 lithium atoms per formula unit (e.g. La3Zr2Li7O12), before the system transitions from a cubic to a tetragonal phase with poor ionic mobility. This arises from full occupation of the Li sites. Hence, the most conductive lithium garnets have Li between 6-6.55 Li per formula unit, which maintains the cubic symmetry and the disordered Li sub-lattice. The tetragonal phase, however, forms the highly conducting cubic phase at higher temperatures, thought to arise from increased cell volume and entropic stabilisation permitting Li disorder. However, little work has been undertaken in understanding the controlling factors of this phase transition, which could enable enhanced dopant strategies to maintain room temperature cubic garnet at higher Li contents. Here, a series of nine tetragonal garnets were synthesised and analysed via variable temperature XRD to understand the dependence of site substitution on the phase transition temperature. Interestingly the octahedral site cation radius was identified as the key parameter for the transition temperature with larger or smaller dopants altering the transition temperature noticeably. A site substitution was, however, found to make little difference irrespective of significant changes to cell volume.
Efficient Surrogates Construction of Chemical Processes: Case studies on Pressure Swing Adsorption and Gas-to-Liquids
Authors: Hao Zhimian , Zhang Chonghuan , Lapkin Alexei
Published: February 2022

We propose a workflow for reduction in the time required for data generation during generation of statistical digital twins. This methodology is particularly relevant for real-world engineering problems when data generation is expensive. A prerequisite for building surrogates is sufficient input/output data, whereas over-sampling can hardly improve the regression accuracy. The time for data generation can be reduced via (1) reduction of the average time spent on generating individual data points and (2) reduction in the total number of data points, by reducing the sampling rate with the improvement of surrogate quality. Examples of a dynamic process and a steady-state process from the field of carbon capture and utilization are used as two case studies: pressure swing adsorption (PSA) and Gas-to-Liquids (GTL). With the proposed methodology, the time for surrogate generation can be reduced by 88% for PSA and 60% for GTL, respectively.
Thermal transport in planar sp2-hybridized carbon allotropes: A comparative study of biphenylene network, pentaheptite and graphene
Authors: Ying Penghua , Liang Ting , Du Yao , Zhang Jin , Zeng Xiaoliang , Zhong Zheng
Published: February 2022

The biphenylene network with periodically arranged four-, six-, and eightmembered rings has been successfully synthesized in very recent experiments. This novel two-dimensional (2D) carbon allotrope has potentials in applications of lithium storage and carbon-based circuitry. Understanding the thermal transport properties of biphenylene network is of critical importance for the performance and reliability of its practical applications. To this end, the thermal transport in biphenylene network is comprehensively investigated in this paper with the aid of molecular dynamics simulations together with first-principles calculations. For the sake of comparison, the thermal conductivities of other 2D sp2-hybridized carbon allotropes including graphene and pentaheptite are also investigated using the same method. It is found that the thermal conductivities of biphenylene network and pentaheptite are, respectively, only about one-thirteenth and one-eighth of graphene. Through the analysis of phonon property, mechanical property and electron density distribution, it is demonstrated that the great reduction in the thermal conductivity of biphenylene network and pentaheptite arises from the decline in their structural symmetry, which leads to the decrease of phonon group velocity and the reduction of phonon mean free path.
Temperature Regulates Stability, Ligand Binding (Mg2+ and ATP) and Stoichiometry of GroEL/GroES Complexes
Authors: Walker Thomas E , Shirzadeh Mehdi , Sun He Mirabel , McCabe Jacob W , Roth Andrew , Moghadamchargari Zahra , Clemmer David E , Laganowsky Arthur , Rye Hays , Russell David H
Published: February 2022

Chaperonins are nanomachines that harness ATP hydrolysis to power and catalyze protein folding, chemical action that is directly linked to the maintenance of cell function through protein folding/refolding and assembly. GroEL and the GroEL-GroES complex are archetypal examples of such protein folding machines. Here, variable-temperature-electrospray ionization (vT-ESI) native mass spectrometry is used to delineate the effects of solution temperature and ATP concentrations on the stabilities of GroEL and GroEL/GroES complexes. The results show clear evidences for de-stabilization of both GroEL14 and GroES7 at temperatures of 50 oC and 45 oC, respectively, substantially below the pre-viously reported melting temperature (Tm ~ 70 oC). This destabilization is accompanied by temperature-dependent reaction products that have previously unreported stoichiometries, viz. GroEL14-GroESx-ATPy, where x = 1, 2, 8 and y = 0, 1, 2, that are also dependent on Mg2+ and ATP concentrations. Variable-temperature native mass spectrometry re-veals new insights about the stability of GroEL in response to several environmental effects: (i) temperature-dependent ATP binding to GroEL (ii) effects of temperature as well as Mg2+ and ATP concentrations on the stoichiome-try of the GroEL-GroES complex, with Mg2+ showing greater effects compared to ATP; and, (iii) a change in the temper-ature-dependent stoichiometries of the GroEL-GroES complex (GroEL14-GroES7 vs GroEL14-GroES8) between 24 to 56 oC. The similarities between results obtained using native MS and cryo-EM (Clare et al., An expanded protein folding cage in the GroEL-gp31 complex. J. Mol. Biol. 2006, 358, 905-11; Ranson et al., Allosteric signaling of ATP hydrolysis in GroEL–GroES complexes. Nat. Struct. Mol. Biol. 2006, 13, 147-152.) underscores the utility of native MS for investiga-tions of molecular machines as well as identification of key intermediates involved in the chaperone-assisted protein folding cycle.
Understanding the Local Chemical Environment of Bioelectrocatalysis
Authors: Edwardes Moore Esther , Cobb Samuel , Coito Ana Margarida , Oliveira Ana Rita , Pereira Ines , Reisner Erwin
Published: February 2022

This work applies electrochemical and computational techniques to explore the local environment of fuel-producing oxidoreductases within porous electrode architectures. This improved understanding of the local environment enabled simple manipulation of the electrolyte solution, by adjusting the bulk pH and buffer pKa, to achieve an optimum local pH for maximal activity of the immobilised enzyme. When applied to macroporous inverse opal electrodes, the benefits of higher loading and increased mass transport were employed and, consequently, the electrolyte adjusted to reach −8.0 mA cm−2 for the H2 evolution reaction (HER) and −3.6 mA cm−2 for the CO2 reduction reaction (CO2RR), demonstrating an 18-fold improvement on previously reported enzymatic CO2RR systems.
Detergent-free functionalisation of hybrid vesicles with membrane proteins using SMALPs
Authors: Catania Rosa , Machin Jonathan , Rappolt Michael , Muench Stephen P. , Beales Paul A. , Jeuken Lars J.C.
Published: February 2022

Hybrid vesicles (HVs) that consist of mixtures of block copolymers and lipids are robust biomimetics of liposomes, providing a valuable building block in bionanotechnology, catalysis and synthetic biology. However, functionalisation of HVs remains laborious and expensive, creating a significant current challenge in the field. Here, using a new approach of extraction with styrene-maleic acid lipid particles (SMALPs), we show that a membrane protein (cytochrome bo3) directly transfers into HVs with an efficiency of 73.9 ± 13.5% and without the requirement of any detergent, long incubation times or mechanical disruption. Interestingly, direct transfer of membrane proteins using this approach was not possible into liposomes. This suggests that the HVs are more amenable than liposomes to membrane protein incorporation from a SMALP system. Finally, we show that this transfer method is not limited to cytochrome bo3 and can also be performed with complex membrane protein mixtures.
Identification of single Ru(II) ions on ceria as a highly active catalyst for abatement of NOx pollutants
Authors: Khivantsev Konstantin , Jaegers Nicholas R. , Aleksandrov Hristiyan A. , Kovarik Libor , Song Inhak , Tian Jinshu , Hernandez Xavier Isidro Pereira , Vayssilov Georgi N. , Wang Yong , Szanyi János
Published: February 2022

Atom trapping allows to prepare catalysts with atomically dispersed Ru ions anchored to the ceria support. The resulting catalysts free of expensive noble metals such as Pt, Pd, Rh (whose prices are ~8-60 times higher than Ru on the per-molar basis) with Ru loadings of only 0.25-0.5 wt% show excellent activity in industrially important catalytic NO oxidation reaction, a critical step that requires use of relatively large loadings of expensive noble metals in diesel aftertreatment systems. Ru1/CeO2 catalysts are stable during continuous cycling, ramping and cooling as well as presence of moisture. Furthermore, Ru1/CeO2 shows excellent NOx storage properties during cold start, with improved NO adsorption compared with the best described Pd/Zeolite NO adsorbers with ~2-3 times higher Pd loadings. We clarify the location of Ru(II) ions on the ceria surface and identify mechanism of NO oxidation (as well as reactive storage) using DFT calculations and in-situ DRIFTS/Mass-spectroscopy measurements. Furthermore, we show the possible applications of Ru1/CeO2 in gasoline engines for NO reduction by CO: only 0.1 wt% of atomically dispersed Ru is sufficient to achieve high activity at low temperatures. With the aid of excitation-modulation in-situ infra-red measurements, we uncover the elementary steps of NO reduction by CO on an atomically dispersed ceria-supported catalyst. Our study highlights the potential applicability of single-atom catalysts to industrially relevant NO and CO abatement.
PoreMatMod.jl: Julia package for in silico post-synthetic modification of crystal structure models
Authors: Henle E. Adrian , Gantzler Nickolas , Thallapally Praveen K. , Fern Xiaoli Z. , Simon Cory M.
Published: February 2022

PoreMatMod.jl is a free, open-source, user-friendly, and documented Julia package for modifying crystal structure models of porous materials such as metal-organic frameworks (MOFs). PoreMatMod.jl functions as a find-and-replace algorithm on crystal structures by leveraging (i) Ullmann's algorithm to search for subgraphs of the crystal structure graph that are isomorphic to the graph of a query fragment and (ii) the orthogonal Procrustes algorithm to align a replacement fragment with a targeted substructure of the crystal structure for installation. The prominent application of PoreMatMod.jl is to generate libraries of hypothetical structures for virtual screenings via molecular simulations. For example, one can install functional groups on the linkers of a parent MOF, mimicking post-synthetic modification. Other applications of PoreMatMod.jl to modify crystal structure models include introducing defects and correcting artifacts of X-ray structure determination (adding missing hydrogen atoms, resolving disorder, and removing guest molecules).
Nonadiabatic Molecular Dynamics by Multiconfiguration Pair-Density Functional Theory
Authors: Calio Paul , Truhlar Don , Gagliardi Laura
Published: February 2022

We present the first implementation of multiconfiguration pair-density functional theory (MC-PDFT) ab initio molecular dynamics. MC-PDFT is a multireference electronic structure method that in many cases has a similar accuracy (or even better accuracy) than complete active space second order perturbation theory (CASPT2) at a significantly lower computational cost. In this work we introduced MC-PDFT analytical gradients into the SHARC molecular dynamics program for ab initio, nonadiabatic molecular dynamics simulations. We verify our implementation by examining the intersystem crossing dynamics of thioformaldehyde, and we observe excellent agreement with recent CASPT2 and experimental findings. Moreover, with MC-PDFT we could perform dynamics with an active space that was computationally too expensive for CASPT2.
Rapid, Presumptive Identification of Seed-Based Toxins using Direct Analysis in Real Time Mass Spectrometry (DART-MS) and its Variants
Authors: Sisco Edward , Damaso Natalie , Robinson Elizabeth L. , Robertson James M. , Forbes Thomas P.
Published: February 2022

Detection of seed-based toxins is a need for forensic chemists when suspected poisonings occur. The evidence that is found is often physically unidentifiable, as the seeds are mashed to extract the toxins. This work investigates potential strategies for rapid detection of seed-based toxins using chemical signatures obtained by direct analysis in real time mass spectrometry (DART-MS). Seven toxins (digoxin, digitoxin, hypaconitine, hyoscyamine, lanatoside, oleandrin, and scopolamine) and six seeds containing these toxins were studied. While detection of four of the toxins was readily attainable, detection of digoxin, digitoxin, and lanatoside was hindered by the inability to thermally desorb these larger compounds under normal operating conditions. The use of DART-MS variants capable of higher temperature analysis (thermal desorption (TD)-DART-MS and infrared thermal desorption ((IRTD)-DART-MS) enabled detection of these compounds. The low-level toxin concentrations and limited number of seeds available for analysis led to detection difficulties from both seed mashes and methanolic seed mash extracts. Principal component analysis (PCA) of generated mass spectra enabled differentiation of seed species, even in the cases when the toxins were undetectable.
The missing piece: The Ti3C2Tx MXene structure and its role in the outstanding reversibility as negative electrode in sodium ion batteries
Authors: Ferrara Chiara , Gentile Antonio , Marchionna Stefano , Quinzeni Irene , Fracchia Martina , Ghigna Paolo , Pollastri Simone , Ritter Clemens , Vanacore Giovanni Maria , Ruffo Riccardo
Published: February 2022

This study proposes the full structural characterization of the most common MXene composition, Ti3C2Tx, which presents outstanding stability as anode for sodium ion batteries (100% of capacity retention after 530 cycles with charge efficiency > 99.7%). The structural investigation is carried out with a multi-technique approach that allows to explore both the short- and long- range structure, combining the analysis of X ray absorption spectroscopy, X-ray and neutron diffraction data, and TEM images. The diffraction data have been analyzed with the approach embodied in the Faults software, that accounts for the evaluation of extended defects, thus allowing to fit, for the first time, the MXene diffraction patterns. The analysis shows that the presence of static disorder on the termination sites induces a variability in the interlayer distance which affects the electrochemical properties.
Photoinduced Collective Motion of Oil Droplets and Concurrent Pattern Formation in Surfactant Solution
Authors: Kojima Tomoya , Kitahata Hiroyuki , Asakura Kouichi , Banno Taisuke
Published: February 2022

Collective motion is ubiquitous in living systems. Although various biomimetic artificial systems have been constructed, there have been few studies reported on collective motion induced by the coupling of chemical reactions, diffusion and convection in a far-from-equilibrium state. In this study, we report an artificial system of oil droplets in a surfactant solution wherein the collective motion of multiple droplets and pattern formation occurred concurrently. Using photo-responsive surfactants with an azobenzene moiety, the assembly of droplets and the formation of circular patterns around the formed droplet clusters occurred under UV illumination, whereas the disassembly of droplets and disappearance of the patterns occurred under subsequent visible light illumination. The observed dynamics were induced by Marangoni flows based on the reversible photoisomerisation of azobenzene-containing surfactants. The phenomena were considered analogous to the bioconvection of microorganisms. These findings could be useful for understanding the mechanism of motion of life in terms of physicochemical aspects.
The Path to Actinorhodin: Regio- and Stereoselective Ketone Reduction by a Type II Polyketide Ketoreductase Revealed in Atomistic Detail
Authors: Serapian Stefano Artin , Crosby John , Crump Matthew P. , van der Kamp Marc W.
Published: February 2022

In type II polyketide synthases (PKSs), which typically biosynthesize several antibiotic and antitumor compounds, the substrate is a growing polyketide chain, shuttled between individual PKS enzymes whilst covalently tethered to an acyl carrier protein (ACP): this requires the ACP interacting with a series of different enzymes in succession. During biosynthesis of the antibiotic actinorhodin, produced by Streptomyces cœlicolor, one such key binding event is between an ACP carrying a 16-carbon octaketide chain (actACP) and a ketoreductase (actKR). Once the octaketide is bound inside actKR, it is likely cyclized between C7 and C12 and regioselective reduction of the ketone at C9 occurs: how these elegant chemical and conformational changes are controlled is not yet known. Here, we perform protein-protein docking, protein NMR, and extensive molecular dynamics simulations to reveal a likely mode of association between actACP and actKR; we obtain and analyze a detailed model of the C7-C12-cyclized octaketide within actKR’s active site; and confirm this model through multiscale (QM/MM) reaction simulations of the key ketoreduction step. Molecular dynamics simulations show that the most thermodynamically stable cyclized octaketide isomer (7S,12R) also gives rise to the most ‘reactive conformations’ for ketoreduction. Subsequent reaction simulations show that ketoreduction is stereoselective as well as regioselective, resulting in an S-alcohol. Our simulations further indicate several conserved residues that may be involved in selectivity of C7-12 cyclisation and C9 ketoreduction. The detailed insights obtained on ACP-based substrate presentation in type II PKSs will help with the design of nonendogenous ACP-ketoreductase systems capable of biosynthesizing non-natural polyketides.
Dual-channel fluorescent probe for the simultaneous monitoring of peroxynitrite and adenosine-5’-triphosphate in cellular applications
Authors: Wu Luling , Liu Jihong , Tian Xue , Groleau Robin , Han Hai-Hao , Sedgwick Adam , Wang Han-Min , Wang Yang , Yang Yonggang , Huang Fang , Bull Steven , Zhang Hua , Huang Chusen , Zhang Yi , Li Jia , He Xiao-Peng , Li Ping , Tang Bo , James Tony , Sessler Jonathan
Published: February 2022

The concentrations of ATP and ONOO− have been correlated with the progression a number of diseases including ischemia-reperfusion injury and drug-induced liver injury. Here, we report the development of fluorescent probe, ATP-LW, which enables the simultaneous detection of ONOO− and ATP. ONOO− selectively oxidises the boronate pinacol ester of ATP-LW, to afford the fluorescent 4-hydroxy-1,8-naphthalimide product NA-OH (λex = 450 nm, λem = 562 nm or λex = 488 nm, λem = 568 nm). While, the binding of ATP to ATP-LW induces the spirolactam ring opening of rhodamine to afford a highly emissive product (λex = 520 nm, λem = 587 nm). Due to the differences in emission between the ONOO− and ATP products, ATP-LW exhibits the unique ability to image ONOO− levels in the green channel (λex = 488 nm, λem = 500-575 nm) and ATP concentrations using the red channel (λex = 514 nm, λem = 575-650 nm). This was demonstrated using hepatocytes (HL-7702 cells) in cellular imaging experiments. The treatment of HL-7702 cell line with oligomycin A (an inhibitor of ATP synthase) resulted in a reduction of ATP in the red channel and increase in ONOO− green channel. While, the presence of SIN-1 (an exogenous ONOO− donor) results in an increase of ONOO−, and decrease in ATP. Significantly, when HL-7702 cells were treated with acetaminophen as a biological model for drug-induced liver injury, an increase in ONOO− green and decrease in ATP red channel fluorescence was observed. These results illustrate the utility of ATP-LW as a chemical tool to simultaneously monitor ATP and ONOO− concentrations in cellular-based applications.
Boosting efficiency in light-driven water splitting by synchronizing reaction and transport processes through dynamic irradiation
Authors: Huber Fabian , Sender Maximilian , Moersch Maximilian , Kaufhold Simon , Ziegenbalg Dirk , Rau Sven
Published: February 2022

This work elaborates the effect of dynamic irradiation and enhanced mass transport on light-driven molecular water oxidation to counteract catalyst deactivation. It highlights the importance of overall reaction design to overcome limiting factors in artificial photosynthesis reactions. Systematic investigation of a homogenous three component ruthenium-based water oxidation system revealed significant potential to enhance the overall catalytic efficiency by synchronizing the timescales of photoreaction and mass transport in a capillary flow reactor. The overall activity could be improved by a factor of more than 10 with respect to the turnover number and a factor of 21 referring to the external energy efficiency by applying low irradiation intensities and high flow rates.
Data-informed reparameterization of modified RNA and the effect of explicit water models: Application to pseudouridine and derivatives
Authors: Dutta Nivedita , Deb Indrajit , Sarzynska Joanna , Lahiri Ansuman
Published: February 2022

Pseudouridine is the most abundant post-transcriptional modification in RNA. We have previously shown that the FF99-derived parameters for pseudouridine and some of its naturally occurring derivatives in the AMBER distribution either alone or in combination with the revised 𝛄 torsion parameters (parmbsc0) failed to reproduce their conformational characteristics observed experimentally (Deb I, et al. J. Chem. Inf. Model. 2014, 54 (4):1129–1142; Deb I, et al. J. Comput. Chem., 2016, 37:1576−1588; Dutta N, et al. J. Chem. Inf. Model. 2020, 60 (10):4995–5002). However, the application of the recommended bsc0 correction did lead to an improvement in the description not only of the distribution in the 𝛄 torsional space but also of the sugar pucker distributions. In an earlier study, we examined the transferability of the revised glycosidic torsion parameters (𝛘IDRP) for Ψ to its derivatives. We noticed that although these parameters in combination with the AMBER FF99-derived parameters and the revised 𝛄 torsional parameters resulted in conformational properties of these residues that were in better agreement with experimental observations, the sugar pucker distributions were still not reproduced accurately. Here we report a new set of glycosidic torsional parameters (𝛘ND) based on glycosidic torsional profiles that correspond to known conformational propensities and a new set of partial atomic charges for pseudouridine, 1-methylpseudouridine, 3-methylpseudouridine and 2′-O-methylpseudouridine and studied their effect on the conformational distributions using REMD simulations at the individual nucleoside level. We have also studied the effect of the choice of water model on the conformational characteristics of these modified nucleosides. Our observations suggest that the current revised set of parameters and partial atomic charges describe the sugar pucker distributions for these residues more accurately and that the choice of a suitable water model is important for the accurate description of their conformational properties.
Investigating the Impact of Solid-Electrolyte Interface on Dendrite Formation: A Case Study Based on Zinc Metal Electrodes
Authors: Gregory Darrell , Britten Collin , Walters Keisha , Çapraz Ömer Özgür
Published: February 2022

The formation of dendrites is the bottleneck to harvest the high theoretical capacities of metal anodes such as Li, Na, Mg, and Zn batteries. The critical current density, interfacial instabilities, and the characteristic of the solid-electrolyte interface (SEI) layer play a major role in the formation mechanisms of dendrites. In this study, we investigated the impact of the SEI layer on the electroplating of zinc metals in organic and aqueous electrolytes by using electrochemical techniques coupled with electron microscopy and X-ray photoelectron spectroscopy. First, the electrochemical response of Zn plating in organic or aqueous electrolytes was compared with the ones for Li and Na metal plating by using analogous perchlorate salt dissolved in the same organic solvent. Under similar charge conditions, the cycle life of the metal electrodes was longer in the order of Zn (aqueous) > Li > Zn (organic) > Na. The impact of the SEI layer is then investigated by electroplating Zn in aqueous for 20 cycles, and then switching it to organic electrolytes and vice versa. In organic electrolytes, the cycle life of the PAO-Zinc is almost three-fold longer than the as-received zinc electrodes. PAO stands for pre-cycled in aqueous electrolyte for twenty times. Overall, our study demonstrated the impact of surface chemistry and morphology on the formation of Zn dendrites. The methodology established here can be used to study the impact of electrolyte salt and additives on the formation of dendrites on metal electrodes.
Bacteria to Control Electron Transport Altering the Synthesis of Non-native Biopolymer
Authors: Bennett Mechelle , Jain Akhil , Kovacs Kaitalin , Hill Phil , Alexander Cameron , Rawson Frankie
Published: February 2022

The use of bacteria as catalysts for radical polymerisations of synthetic monomers has recently been established. However, the role that transplasma membrane electron transport (tPMET) plays in modulating these processes is not well understood. We sort to study this by genetic engineering of a part of a tPMET system NapC in E. coli and show this altered the rate of extracellular electron transfer and caused an effect on cell-mediated polymerisation using a model monomer. A plasmid with arabinose inducible PBAD promoters were shown to upregulate NapC protein upon arabinose induction at total arabinose concentrations of 0.0018% and 0.18%. These clones (E. coli (IP_0.0018%) and E. coli (IP_0.18%), respectively) were used in Fe atom transfer radical polymerization (ATRP), revealing faster polymerization rates than cultures containing suppressed or empty plasmids (E. coli (IP_S) and E. coli(E), respectively). These results lead to the hypothesis that EET (Extracellular Electron Transfer) mechanisms in part modulate rates of ATRP iron-mediated cell instructed polymerizations.
Proteoform-selective imaging of tissues using mass spectrometry
Authors: Yang Manxi , Hu Hang , Su Pei , Thomas Paul M. , Camarillo Jeannie M. , Greer Joseph B. , Early Bryan P. , Fellers Ryan T. , Kelleher Neil L. , Laskin Julia
Published: February 2022

Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform-specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) for the proteoform-selective imaging of biological tissues. Nano-DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof-of-concept experiments demonstrate that nano-DESI MSI combined with on-tissue top-down proteomics is ideally suited for the proteoform-selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain.
A Broadly Applicable Alkyl-Alkyl Suzuki-Miyaura Cross-Coupling Reaction Catalyzed by an Iron-Based Complex
Authors: Tyrol Chet , Byers Jeffery
Published: February 2022

An iron-based catalyst for the Suzuki-Miyaura reaction between two sp3-hybridized substrates has been developed for a broad range of unactivated alkyl halides and alkyl boranes. Key to success was using a Cs-symmetric beta-diketiminate ligand that contained a tert-butyl and trifluoromethyl functionalized backbone. The breadth of the cross-coupling reaction was demonstrated with high yields of cross-coupled products observed from reactions using primary and secondary alkyl bromides as well as primary alkyl boranes and even some secondary alkyl boranes. Complementary methylation reactions using methyl iodide or methyl-9-BBN was also possible. The facile diversification of a steroid derivative using these reactions demonstrated the synthetic utility of such complementary cross coupling reactions.
Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach
Authors: Lucas Kenneth , Chen Amy , Schubmehl Megan , Kolonko Kristopher J. , Barnes George L.
Published: February 2022

We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of L-lysine-H$^+$ and its side-chain methylated analogues, $N_\epsilon$-Methyl-L-lysine-H$^+$ (\methylLysH{1}), $N_\epsilon$,$N_\epsilon$-Dimethyl-L-lysine-H$^+$ (\methylLysH{2}), and $N_\epsilon$,$N_\epsilon$,$N_\epsilon$-Trimethyl-L-lysine-H$^+$ (\methylLysH{3}). The major pathways observed in the experimental measurements were \mz 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The \mz 130 peak corresponds to loss of N(CH$_3$)$_n$H$_{3-n}$ while \mz 84 has the additional loss of H$_2$CO$_2$ likely in the form of H$_2$O+CO. Within the time frame of the direct dynamics simulations, \mz 130 and 101 were the most populous peaks, with the latter identified as an intermediate to \mz 84. The simulations allowed for the determination of several reaction pathways that result in these products. A graph theory analysis enabled the elucidation of the significant structures that compose each peak. Methylation results in the preferential loss of the side-chain amide group and a reduction of cyclic structures within the \mz 84 peak population in simulations.
Understanding the Mechanism of Plasmon-Driven Water Splitting: Hot Electron Injection and Near Field Enhancement Effects
Authors: Huang Jiaquan , Zhao Xinyi , Huang Xunkun , Liang Wanzhen
Published: February 2022

Utilizing plasmon-generated hot carriers to drive chemical reactions has currently become an active area of research in solar photocatalysis at the nanoscale. However, the mechanism underlying exact transfer and the generation dynamics of hot carriers, and the strategies used to further improve the quantum efficiency of the photocatalytic reaction still deserve a further look. In this work, we perform a nonadiabatic excited-state dynamics study to depict the correlation between the reaction rate of plasmon-driven water splitting (PDWS) and the sizes of gold particles, the incident light frequency and intensity, and the near-field's spatial distribution. Four model systems, \ce{H2O} and \ce{Au20}@\ce{H2O} separately interacting with the laser field and the near field generated by the Au nanoparticle (NP) with a few nanometers in size, have been investigated. Our simulated results clearly unveil the mechanism of PDWS and hot-electron injection in a Schottky-free junction: the electrons populated on the antibonding orbitals of \ce{H2O} are mandatory to drive the \ce{OH} bond breaking and the strong orbital hybridization between \ce{Au20} and \ce{H2O} creates the condition for direct electron injection. We further find that the linear dependence of the reaction rate and the field amplitude only holds at a relatively weak field and it breaks down when the second {\ce{OH}} bond begins to dissociate and field-induced water fragmenting at a very intensive field, and that with the guarantee of electron injection, the water splitting rate increases with the increase of NP's size. This study will be helpful for further improving the efficiency of the photochemical reactions involving the plasmon-generated hot carriers and expanding the applications of hot carriers in varieties of chemical reactions.
National Institutes of Health (NIH) Workshop on Reaction Informatics
Authors: Warr Wendy
Published: February 2022

The virtual workshop took place on May 18-20, 2021. It was a follow-up from the December 2020 NIH Workshop on Ultra Large Chemistry Databases. A major theme emerging from the December 2020 workshop was the fact that all the databases of a billion or more structures are virtual. For each virtual molecule the question then arises of whether, or how, it can be synthesized. The organizers therefore assembled speakers to give presentations about how reaction-related data are represented, captured, managed in databases, analyzed, used for drug design, applied in robotics, and exchanged locally as well as globally. This report summarizes talks from 27 practitioners in the reaction informatics field. The aim is to represent as accurately as possible the information that was delivered by the speakers; the report does not seek to be evaluative. The themes, in the order used for this report, were reaction representations, file formats, and standards; sources of reaction data; AI and machine learning applications of reaction-related data in de novo drug design, synthetic accessibility, synthesis planning, reaction prediction etc.; and automation and progression toward autonomous synthesis.
Ordering of Small Molecules on Hydrophobic Self-Assembled n-Alkanethiols: Delicate Balance of Interfacial and Intermolecular Interactions
Authors: Ghosh Mithun , Yang Ding-Shyue
Published: February 2022

Growth of molecular thin films with desired orders and orientations has become technologically relevant as the electronic industries seek new opportunities and applications. However, the delicate balance of interfacial and intermolecular forces and their complex influence on thin-film growths still require more understanding. Here, the effects of a hydrophobic self-assembled monolayer (SAM) surface on the crystallization of four common solvents—acetonitrile, ethanol, methanol, and water—are investigated. Despite the absence of significant substrate–molecule forces, unexpected oriented growth is observed for these molecules except water. Acetonitrile and ethanol form a sustaining vertical assembly order with long-range crystalline structures. Coincident epitaxy with small lattice mismatches is found to be essential to these orderings, which are energetically favored but without a dominant azimuthal orientation. In contrast, a preferred in-plane registry of methanol overlayers is observed for an ultrathin nominal thickness and becomes lost in slightly thicker films. Such thickness-dependent ordering of methanol assemblies can be explained with semi-commensurate epitaxy with a tensile strain of ~6.6% along hydrogen-bonded chains, whose quick relief results in the loss of order and even the phase. These rich observations suggest that SAM surfaces offer good opportunities for selective crystallization of molecular films worthy of further investigations.
Co(II) Amide, Pyrrolate, and Aminopyridinate Complexes: Assessment of their Manifold Structural Chemistry and Thermal Properties
Authors: Zanders David , Boysen Nils , Land Michael A. , Obenlüneschloß Jorit , Masuda Jason D. , Mallick Bert , Barry Seán T. , Devi Anjana
Published: February 2022

A series of cobalt(II) (silyl)amides, pyrrolates and aminopyridinates were synthesized. Inspired by the dimeric bis(trimethylsilylamido)cobalt(II) complex ([Co(TMSA)2]2), facile salt metathesis employing the ligand 2,2,5,5-tetramethyl-1,2,5-azadisilolidinyl (TMADS) yielded its congener [Co(TMADS)2]2. Novel, heteroleptic Lewis adducts of the former resulted in unusual three- to four-fold coordination geometry around the metal center. Similarily, the salt [Co(TMADS)3Li(DAD)2] was isolated which demonstrates an ion separated Co(II) anion with silylamide ligation and Li+ counter cation. Transpyrrolylation using [Co(TMSA)2]2 was established for the synthesis of bis[N,N’-2-(dimethylaminomethyl)pyrrolyl]cobalt(II), and bis(N-2-(tert-butyliminomethyl)pyrrolyl)cobalt(II). Treatment of CoCl2 with two equivalents of lithiated N,N-dimethyl(N’-tert-butyl)ethane-1-amino-2-amide and N,N-dimethyl(N’-trimethylsilyl)ethane-1-amino-2-amide resulted in the respective Co(II) amido-amines. Reaction of CoCl2 with lithium 4-methyl-N-(trimethylsilyl)pyridine-2-amide yielded the first binuclear, homoleptic Co(II) aminopyridinate complex with a distorted trigonal bipyramidal coordination environment (τ5 = 0.533) for one central Co(II) ion and a weakly distorted tetrahedral coordination geometry (τ4 = 0.845) for the other. All of the new compounds were thoroughly characterized in terms of composition and structure. Finally, the key thermal characteristics of volatility and thermal stability were assessed using a combination of thermogravimetric analysis and complementary bulk sublimation experiments.
Real Molecular Structure and its Canonical Forms Explanation in Resonance Theory, through Comparison Analogy of Real Macro Entity and its Different Sketches
Authors: ahmed faiz
Published: February 2022

In elementary chemistry courses students often demonstrate difficulty with real understanding of Resonance Theory i.e. canonical structure vs. real molecule difference, so unanswered puerile questions during lecture made the subject boring. Particularly students unable to understand the difference between a real microscopic moiety and it’s proposed sketch or model at early stages of their learning. In such situations use of suitable analogy other than the subject area make the teaching more effective. Using an analogy from the daily life act as a powerful tool to explain curious questions efficiently to develop the interest of the students in subject. Sharing of personal experiences and analogies among scientific community is an effective way to spread scientific knowledge magnificently.
Significance of Suitable Analogy Usage to Explain Challenging Theories in Chemistry and Other Fields of Science
Authors: ahmed faiz
Published: February 2022

In elementary chemistry courses students often demonstrate difficulty with real understanding of Resonance Theory i.e. canonical structure vs. real molecule difference, so unanswered puerile questions during lecture made the subject boring. Particularly students unable to understand the difference between a real microscopic moiety and it’s proposed sketch or model at early stages of their learning. In such situations use of suitable analogy other than the subject area make the teaching more effective. Using an analogy from the daily life act as a powerful tool to explain curious questions efficiently to develop the interest of the students in subject. Sharing of personal experiences and analogies among scientific community is an effective way to spread scientific knowledge magnificently.
A multiple time step algorithm for trajectory surface hopping simulations
Authors: Baudin Pablo , Ursula Roethlisberger
Published: February 2022

A multiple time step (MTS) algorithm for trajectory surface hopping molecular dynamics has been developed, implemented, and tested. The MTS scheme is an extension of the ab initio implementation for Born{Oppenheimer molecular dynamics presented in [J. Chem. Theory Comput. 14, 2834 (2018)]. In particular, the MTS algorithm has been modi�ed to enable the simulation of non-adiabatic processes with the trajectory surface hopping (TSH) method and Tully's fewest switches algorithm. The speci�al feature of the implementation lies in the combination of Landau-Zener and Tully's transition probabilities during the inner MTS time steps. The new MTS-TSH method is applied successfully to the photorelaxation of protonated formaldimine, showing that the important characteristics of the process are recovered by the MTS algorithm. A computational speed-up between 1.5 and 3 has been obtained compared to standard TSH simulations which is close to the ideal values that could be obtained with the computational settings considered.
Ultra Low-cost DNA Miniprep Spin-Columns for Rapid Filter-Trapped Proteomics Sample Preparation
Authors: Mousseau Campbell , Pierre Camille , Champion Matthew
Published: February 2022

Complete proteolytic digestion in the preparation of proteins for bottom-up proteomic analysis is substantially improved by the use of detergents for complete denaturation. This however is incompatible with many proteases, and highly detrimental to LC-MS/MS data collection. Recently, filter-based methods such as FASP (Filter-Aided Sample Prep) have seen wide use due to their ability to remove detergents and other harmful reagents prior to digestion and mass spectrometric analysis. Unfortunately, these techniques can be variable and time consuming. Suspension trapping (S-Trapping) is a newer method that utilizes a depth-filter to trap flocculated proteins, and has proven to be a faster approach for proteomic analysis. Sample preparation by these methods requires careful control of protein concentrations in order to flocculate the sample for collection, and the cost of commercial solutions can be high. We hypothesized that protein suspensions also retain on silica-based filters due to ionic interactions mediated by the presence of sodium (Na+), SO42- and PO43-. As such, we sought to investigate if very low-cost DNA purification spin-filters, so called ‘minipreps’ could efficiently and reproducibly trap proteins for digest and LC-MS/MS analysis. Using model proteins and whole-cell lysates we compared digestion efficiencies, capacities, recovery and identification rates from samples prepared using DNA-minipreps and FASP-based protocols. Samples were analyzed using nano uHPLC MS-MS/MS and Label-Free-Quantitative (LFQ) proteomics. DNA-filters show low variability, excellent recovery, sensitivity, and proteome depth from a commercially obtainable device which costs < $0.25 (US) per sample.
Following Molecular Mobility During Chemical Reactions: No Evidence for Active Propulsion
Authors: Fillbrook Lucy , Günther Jan-Philipp , Majer Günter , O'Leary Daniel , Price William , Van Ryswyk Hal , Fischer Peer , Beves Jonathon
Published: February 2022

The measured changes in self-diffusion of small molecules during reactions have been attributed “boosted mobility”. We demonstrate the critical role of changing concentrations of paramagnetic ions on nuclear magnetic resonance (NMR) signal intensities, which lead to erroneous measurements of diffusion coefficients. We present simple methods to overcome this problem. The use of shuffled gradient amplitudes allows accurate diffusion NMR measurements, even with time-dependent relaxation rates caused by changing concentrations of paramagnetic ions. The addition of a paramagnetic relaxation agent allows accurate determination of both diffusion coefficients and reaction kinetics during a single experiment. We analyze a copper-catalyzed azide-alkyne cycloaddition ‘click’ reaction, for which boosted mobility has been claimed. With our methods, we accurately measure the diffusive behavior of solvent, starting materials and product, and find no global increase in diffusion coefficients during the reaction. We overcome NMR signal overlap using an alternative reducing agent to improve the accuracy of the diffusion measurements. The alkyne reactant diffuses slower as the reaction proceeds, due to binding to the copper catalyst during the catalytic cycle. The formation of this intermediate was confirmed by complementary NMR techniques and density functional theory calculations. Our work calls into question recent claims that molecules actively propel or swim during reactions, and establishes that time-resolved diffusion NMR measurements can provide valuable insight into reaction mechanisms.