bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling amphiphilic polymer folding beyond the primary structure with protein-mimetic di(phenylalanine)
Authors: Warren Jacqueline L. , Dykeman-Bermingham Peter , Knight Abigail
Published: February 2022

While methods for polymer synthesis have proliferated, their functionality pales in comparison to natural biopolymers – strategies are limited for building the intricate network of noncovalent interactions necessary to elicit complex, protein-like functions. Using a bioinspired di(phenylalanine) acrylamide (FF) monomer, we explored the impact of various non-covalent interactions in generating ordered assembled structures. Amphiphilic copolymers were synthesized that exhibit β-sheet-like local structure upon collapsing into single-chain assemblies in aqueous environments. Systematic analysis of a series of amphiphilic copolymers illustrated that the global collapse is primarily driven by hydrophobic forces. Hydrogen-bonding and aromatic interactions stabilize local structure, as β-sheet-like interactions were identified via circular dichroism and thioflavin T fluorescence. Similar analysis of phenylalanine (F) and alanine-phenylalanine acrylamide (AF) copolymers found that distancing the aromatic residue from the polymer backbone is sufficient to induce β-sheet-like local structure akin to the FF copolymers; however, the interactions between AF subunits are less stable than those formed by FF. Further, hydrogen-bond donating hydrophilic monomers disrupt internal structure formed by FF within collapsed assemblies. Collectively, these results illuminate design principles for the facile incorporation of multiple facets of protein-mimetic, higher-order structure within folded synthetic polymers.
Modified Born-Lande Equation to calculate Lattice Energy in a theoretical approach
Authors: Gupta Aakash , Jana Debasis
Published: February 2022

Defects in ionic solid are very much common, which is increased with the rise in temperature. It causes the change in the value of many physical properties and varieties of physical parameters and the Lattice Energy is one such parameter to control the physical properties of the crystals. Considering the loss of ions from lattice points as random, the examination of each of the defects individually is going to be unpredictable, thus leading to almost nonattainment of the correct crystal structure with the theoretical calculations applying for available models. Here, in this present work, we have used some statistical methods and probabilistic approximation to introduce a novel idea of calculating the Madelung constant, and then Lattice Energy analytically. To make the understanding more lucid, we have taken one of the very common crystals, very popular in the crystallographic community, NaCl crystal having 6:6 co-ordination number, for which a significant number of Schottky defects are observed. During this study, we are bound to assume the random distribution of defects as Poisson distribution due to the fact that the number of defects is very less with respect to the total numbers of lattice points present in the crystal to calculate the Madelung Constant.
Commercial-Scale Visible-light Trifluoromethylation of 2-Chlorothiophenol using CF3I gas.
Authors: Harper Kaid , Grieme Timothy , Towne Timothy , Mack Daniel , Diwan Moiz , Ku Yi-Yin , Griffin Jeremy , Miller Robert , Zhang En-xuan , Liu Zhi-qing , Zheng Song-yuan , Zhang Ning-ning , Grangula Srinivas , Yuan Jia-long , Huang Ping-zhong , Gage James
Published: February 2022

Despite the growth of photoredox methods in academia, application of photoredox at scale in the pharmaceutical and fine chemical industries has been slow. In this report, a photoredox trifluoromethylation of a thiophenol was modified from the original literature report and the mechanism was investigated to define key scale-up parameters. The mechanistic insight was leveraged in the design and execution of two different reactor designs: an LED-based plug flow photoreactor as well as a laser-based continuous stirred tank photoreactor. In one of the first examples of commercial scale photoredox chemistry, the process was scaled to provide over 500 kilograms of the desired intermediate and amended to fully continuous manufacturing.
On-chip Direct Laser Writing of PAN-based Carbon Supercapacitor Electrodes
Authors: Hoffmann Andreas , Jiménez-Calvo Pablo , Strauss Volker , Kühne Alexander
Published: February 2022

We report carbonization of polyacrylonitrile by direct laser writing to produce microsupercapacitors directly on-chip. We demonstrate the process by producing interdigitated carbon finger electrodes directly on a printed circuit board, which we then employ to characterize our supercapacitor electrodes. By varying the laser power, we are able to tune the process from carbonization to material ablation. This allows to not only convert pristine polyacrylonitrile films into carbon electrodes, but also to pattern and cut away non-carbonized material to produce completely freestanding carbon electrodes. While the carbon electrodes adhere well to the printed circuit board, non-carbonized polyacrylonitrile is peeled off the substrate. We achieve specific capacities as high as 260 µF/cm2 in a supercapacitor with 16 fingers.
Plasmon Character Index: An Accurate and Efficient Metric for Identifying and Quantifying Plasmons in Molecules
Authors: Langford James , Xu Xi , Yang Yang
Published: February 2022

Plasmons, which are collective and coherent oscillations of charge carriers driven by an external field, play an important role in applications such as solar energy harvesting, sensing, and catalysis. Plasmons can be found in bulk and nanomaterials, and in recent years, plasmons have also been identified in molecules and these molecules have been utilized to build plasmonic devices. As molecular plasmons can no longer be described by classical electrodynamics, a description using quantum mechanics is necessary. Many methods have been developed to identify and quantify molecular plasmons based on the properties of plasmonic excitations. However, there is not currently a method that is widely accepted, connects to collectivity and coherence, and is computationally practical. Here we develop a metric to accurately and efficiently identify and quantify plasmons in molecules. A number, which we call plasmon character index (PCI), can be calculated for each electronic excited state and describes the plasmonicity of the excitation. PCI is developed from the collective and coherent excitation picture in orbitals and shows excellent agreement with the predictions from scaled time-dependent density functional theory but is vastly more computationally efficient. Therefore, PCI can be a useful tool in identifying and quantifying plasmons and will inform the rational design of plasmonic molecules and small nanomaterials.
Force–Field–Based Computational Study of the Thermodynamics of a Large Set of Aqueous Alkanolamine Solvents for Post–Combustion CO2 Capture
Authors: Noroozi Javad , Smith William
Published: February 2022

The ability to predict the thermodynamic properties of amine species in CO$_2$-loaded aqueous solutions, including their deprotonation (p\textit{K$_a$}) and carbamate to bicarbonate reversion (p\textit{K$_c$}) equilibrium constants and their corresponding standard reaction enthalpies, is of critical importance for the design of improved carbon capture solvents. In this study, we used isocoulombic forms of both reactions to determine these quantities for a large set of aqueous alkanolamine solvent systems. Our hybrid approach involves using classical molecular dynamics simulations with the General Amber Force Field (GAFF) and semi--empirical AM1--BCC charges (GAFF/AM1--BCC) in the solution phase, combined with high level composite quantum chemical ideal-gas calculations. We first determined a new force--field (FF) for the hydronium ion (H$_3$O$^+$) by matching to the single experimental (p\textit{K$_a$}) data point for the well--known MEA system at 298.15 K. We then used this FF to predict the p\textit{K$_a$} values for 76 other amines at 298.15 K and for all 77 amines at elevated temperatures. Additionally, we indirectly relate the H$_3$O$^+$ hydration free energy to that of H$^+$, and provide expressions for intrinsic hydration free energy and enthalpy of the proton. Using the derived H$_3$O$^+$ FF, we predicted the (p\textit{K$_a$}) values of a diverse set of alkanolamines with an overall AAD of less than 0.72 p\textit{K$_a$} units. Furthermore, the derived H$_3$O$^+$ force field is able to predict the protonation enthalpy of these amines when used with the GAFF. We also predicted the carbamate reversion constants of the primary and secondary amine species in the data set and their corresponding standard heats of reaction, which we compared with the scarcely available experimental data, which are often subject to significant uncertainty. Finally, we also described the influence of electronic and steric of different molecular fragments/groups on the stabilities of the carbamates.
Spatial control of heat flow at the nanoscale using Janus particles
Authors: Olarte-Plata Juan D. , Gabriel Jordan , Albella Pablo , Bresme Fernando
Published: February 2022

Janus Nanoparticles (JNP) feature heterogeneous compositions bringing opportunities in technological and medical applications. We investigate using non-equilibrium molecular dynamics simulations the temperature field generated around heated spherical Janus Nanoparticles to assess the performance of the particles in the generation of anisotropic heating. We demonstrate that the contrasting interfacial thermal conductances of the fluid-material interfaces arising from the heterogeneous composition of the JNP can be exploited to control the thermal fields around the nanoparticle leading to a temperature difference between both sides of the nanoparticle (temperature contrast) that is significant for particles comprising regions with disparate hydrophilicity. We illustrate this idea using simplified atomistic and complex models of gold nanoparticles passivated with hydrophobic and hydrophilic ligands in water. Furthermore, we introduce a continuum model to predict the temperature contrast as a function of the interfacial thermal conductance and nanoparticle size. We further show that, unlike homogeneous nanoparticles, the interfacial fluid temperature depends on the interfacial thermal conductance of Janus nanoparticles.
Investigating Novel Thiazolyl-Indazole Derivatives as Scaffolds for SARS-Cov-2 MPro Inhibitors
Authors: Airas Justin , Bayas Catherine A. , N'Ait Ousidi Abellah , Ait Itto My Youssef , Auhmani Aziz , Loubidi Mohamed , Esseffar M'hamed , Pollock Julie A. , Parish Carol A.
Published: February 2022

COVID-19 is a global pandemic caused by infection with the SARS-CoV-2 virus. Remdesivir, a SARS-CoV-2 RNA polymerase inhibitor, is the only drug to have received widespread approval for treatment of COVID-19. The SARS-CoV-2 main protease enzyme (MPro), essential for viral replication and transcription, remains an active target in the search for new treatments. In this study, the ability of novel thiazolyl-indazole derivatives to inhibit MPro is evaluated. These compounds were synthesized via the heterocyclization of phenacyl bromide with (R)-carvone and (R)-pulegone thiosemicarbazones. The binding affinity and atomistic interactions of each compound were evaluated through Schrödinger Glide docking, AMBER molecular dynamics simulations, and MM-GBSA free energy estimation, and these results were compared with similar calculations of MPro binding various 5-mer substrates (VKLQA, VKLQS, VKLQG). From these simulations, we can see that binding is driven by residue specific interactions such as π-stacking with His41, and S/π interactions with Met49 and Met165. The compounds were also experimentally evaluated in a MPro biochemical assay and the most potent compound containing a phenylthiazole moiety inhibited protease activity with an IC50 of 92.9 µM. This suggests that the phenylthiazole scaffold is a promising candidate for the development of future MPro inhibitors.
Investigating Novel Thiazolyl-Indazole Derivatives as Scaffolds for SARS-CoV-2 MPro Inhibitors
Authors: Airas Justin , Bayas Catherine A. , N'Ait Ousidi Abdellah , Ait Itto My Youssef , Auhmani Aziz , Loubidi Mohamed , Esseffar M'hamed , Pollock Julie A. , Parish Carol A.
Published: February 2022

COVID-19 is a global pandemic caused by infection with the SARS-CoV-2 virus. Remdesivir, a SARS-CoV-2 RNA polymerase inhibitor, is the only drug to have received widespread approval for treatment of COVID-19. The SARS-CoV-2 main protease enzyme (MPro), essential for viral replication and transcription, remains an active target in the search for new treatments. In this study, the ability of novel thiazolyl-indazole derivatives to inhibit MPro is evaluated. These compounds were synthesized via the heterocyclization of phenacyl bromide with (R)-carvone and (R)-pulegone thiosemicarbazones. The binding affinity and atomistic interactions of each compound were evaluated through Schrödinger Glide docking, AMBER molecular dynamics simulations, and MM-GBSA free energy estimation, and these results were compared with similar calculations of MPro binding various 5-mer substrates (VKLQA, VKLQS, VKLQG). From these simulations, we can see that binding is driven by residue specific interactions such as π-stacking with His41, and S/π interactions with Met49 and Met165. The compounds were also experimentally evaluated in a MPro biochemical assay and the most potent compound containing a phenylthiazole moiety inhibited protease activity with an IC50 of 92.9 µM. This suggests that the phenylthiazole scaffold is a promising candidate for the development of future MPro inhibitors.
Lowering the C-H Bond Activation Barrier of Methane Using SAC@Cu(111): A Periodic DFT Investigations
Authors: Bhati Meema , Dhumal Jignesh , Joshi Kavita
Published: February 2022

Methane has long captured the world's spotlight for being the simplest and yet one of the most notorious hydrocarbon. Exploring its potential to be converted into value added products has raised a compelling interest. In the present work, we have studied the efficiency of Single-Atom Catalysts (SACs) for methane activation employing Density Functional Theory (DFT). The Climbing Image-Nudged Elastic Bond (CI-NEB) method is used in tandem with the Improved Dimer (ID) method to determine the minimum energy pathway for the first C-H bond dissociation of methane. Our study reported that the transition-metal doped Cu(111) surfaces enhance adsorption, activate C-H bond, and reduce activation barrier for first C-H bond cleavage of methane. The results suggest Ru/Co/Rh doped Cu(111) as promising candidates for methane activation with minimal activation barrier and less endothermic reaction. For these SACs, the calculated activation barriers for first C-H bond cleavage are 0.17 eV, 0.24 eV, and 0.26 eV respectively, which is substantially lower than 1.13 eV, the activation barrier for Cu(111).
Frank-van der Merwe Growth in Bilayer Graphene
Authors: Wang Haozhe , Yao Zhenpeng , Jung Gang Seob , Song Qichen , Hempel Marek , Palacios Tomas , Chen Gang , Buehler Markus J. , Aspuru-Guzik Alan , Kong Jing
Published: February 2022

Bilayer graphene has attracted significant interest due to its unique properties, including fascinating electrical behavior when one layer is slightly rotated relative to the other. However, the quality of large-area bilayer graphene is often limited by the layer-plus-island growth mode in which islands of thicker graphene present as unavoidable impurities. Here, we report the observation of the layer-by-layer, Frank-van der Merwe (FM) growth mode in bilayer graphene where multilayer impurities are suppressed. Instead of the conventional surface adhesive energy, it is found that interface adhesive energy is possible to be tuned with an oxidative pretreatment. The FM-grown bilayer graphene is of AB-stacking or with small-twisting-angle (θ = 0-5°), which is more mechanically robust compared to monolayer graphene, facilitating a free-standing wet transfer technology.
Conduction of Electric Current to Organic Molecules observed by Carrier Transport Mobility Measurements
Authors: Komatsu Toshiki
Published: February 2022

Organic semiconductors have been studied for many years, but electric current conduction through organic materials has proven difficult in practice. To evaluate the carrier mobility of newly synthesized modified polyacenes, we prepared suitable techniques for determining the physical properties of the polyacenes from electrical measurements. In a transparent electrode cell based on a low-melting-point material, we observed the dark-current dependence on the cooling rate and evaluated the sample impurity. We then developed a vertical field-effect transistor (FET) device for high- melting-point materials that easily measures the transconductance of a single drop of a sample solution. The vertical FET device provides indirect evidence of Marcus’ theory of electric conduction phenomena in aggregated organic materials.
Efficient Electrosynthesis of White Phosphorus from Molten Condensed Phosphate Salts
Authors: Melville Jonathan , Licini Andrew , Surendranath Yogesh
Published: February 2022

Elemental white phosphorus (P4) is a crucial feedstock for the entire phosphorus-derived chemicals industry, spanning everything from herbicides to food additives. Currently, industrial P4 production is gated by the infrastructurally demanding reduction of phosphate rock by carbon coke in an arc furnace at temperatures of up to 1500 °C. The electrochemical reduction of phosphate salts could enable the sustainable, point-of-use manufacture of white phosphorus; however, such P4 electrosynthesis requires the rapid activation of strong P—O bonds. Herein, we show that the intrinsic oxide-accepting character of phosphoryl anhydride linkages in molten condensed phosphate salts promotes the reduction of phosphate to white phosphorus at high electron and energy efficiencies. These findings could enable an efficient, low-carbon alternative to legacy carbothermal synthesis of P4.
Separation of disaccharide epimers, anomers and connectivity isomers by high resolution differential ion mobility mass spectrometry
Authors: Mastellone Jordan , Kabir K M Mohibul , Huang Xiaojing , Donald William
Published: February 2022

Glycans are ubiquitous, structurally diverse molecules that have specific and general roles involving metabolism, structure, and cell-to-cell signalling. Functional specificity depends strongly on the complexity of structures that polysaccharides can adopt based on their subunit composition, length, extent of branching, glycosidic bond connectivity and anomeric configuration. However, a rapid and comprehensive characterization of glycan isomers can be challenging owing to limitations associated with their separation. Here, ten composition, anomeric and connectivity disaccharide isomers were separated and detected using high-resolution differential ion mobility-mass spectrometry (DMS-MS, also known as FAIMS). Focus was primarily directed to compositional isomers corresponding to epimers that differ by the axial or equatorial position of a single hydroxyl group. DMS resolving power was enhanced 15-fold primarily by increasing the fraction of helium in the ion carrier gas and lowering the flow rate. At relatively high disaccharide concentrations, DMS-MS of each disaccharide resulted in complex and unique multi-peak spectra with up to ten fully and partially resolved peaks for β-1,4-mannobiose (Man-1,4β-Man), which can be attributed to the DMS separation and subsequent dissociation of ionic non-covalently bound oligomers into monomer ions. Each DMS spectrum has at least one differentiating peak that is not in the other spectra, indicating that DMS can be used to fully or partially resolve composition, configuration and connectivity isomers. At relatively low disaccharide concentrations, disaccharide epimers can also be readily separated by DMS. The integration of high-resolution, ambient pressure DMS with complementary reduced-pressure ion mobility and MS-based glycomics and glycoproteomics workflows may be useful for improving the characterization of glycans and glycosylated biomolecules.
On the dynamics in chemical vapor deposition of InN
Authors: Hsu Chih-Wei , Deminskyi Petro , Persson Anton , Karlsson Matts , Pedersen Henrik
Published: February 2022

Epitaxial, nanometer-thin indium nitride (InN) films are considered as promising active layers in various device applications but remains challenging to deposit. We compare the morphological evolution and characterizations of InN films with various growth conditions in chemical vapor deposition (CVD), by both a plasma atomic layer deposition (ALD) approach and a conventional metalorganic CVD approach. Our results, and previous literature, show that a time-resolved precursor supply is highly beneficial for deposition of smooth and continuous InN nanometer-thin films. We show that the time for purging the reactor between the precursor pulses and low deposition temperature are key factors to achieve homogeneous InN. Our study suggests that 320 °C is the upper temperature where the dynamics of the deposition chemistry can be controlled to involve only surface reactions with surface species. The results highlight the promising role of the ALD technique in realizing electronic devices based on nanometer-thin InN layers.
Exploring the Relationship between the CO Oxidation Reaction and the Elemental Composition in Electrocatalysts with Machine Learning - a Case Study of PtRuPdRhAu High Entropy Alloys
Authors: Mints Vladislav , Pedersen Jack , Bagger Alexander , Quinson Jonathan , Rossmeisl Jan , Arenz Matthias
Published: February 2022

In recent years, the development of complex multi-metallic nanomaterials like high entropy alloy (HEA) catalysts has gained popularity. Composed of 5 or more metals, the compositions of HEAs exhibit extreme diversity. This is both a promising avenue to identify new catalysts and a severe constraint on their preparation and study. To address the challenges related to the preparation, study and optimization of HEAs, machine learning solutions are attractive. In this paper, the composition of PtRuPdRhAu hydrogen oxidation catalysts is optimized for the CO oxidation reaction. This is achieved by constructing a dataset using Bayesian optimization as guidance. For this quinary nanomaterial, the best performing composition was found within the first 35 experiments. However, the dataset was expanded until a total of 68 samples were investigated. This final dataset was used to construct a random forest regression model and a linear model. These machine learned models were used to assess the relationships between the concentrations of the consituent elements and the CO oxidation reaction onset potential. The onset potentials were found to correlate with the composition dependent adsorption energy of *OH obtained from density functional theory. This study demonstrates, how machine learning can be employed in an experimental setting to investigate the vast compositional space of HEAs.
Organophotocatalytic Late-stage N-CH3 Oxidation of Trialkylamines with O2 in Continuous Flow
Authors: Mandigma Mark J. P. , Zurauskas Jonas , MacGregor Callum I. , Edwards Lee J. , Shahin Ahmed , d'Heureuse Ludwig , Yip Philip , Birch David J. S. , Gruber Thomas , Heilmann Jörg , John Matthew P. , Barham Joshua P.
Published: February 2022

We report an organophotocatalytic, N-CH3-selective oxidation of trialkylamines in continuous flow. Based on the 9,10-dicyanoanthracene (DCA) core, a new catalyst (DCAS) was designed with solubilizing groups for processing in flow which allowed harnessing of O2 as a benign reagent for late-stage photocatalytic N-CH3 oxidation of natural products and active pharmaceutical ingredients. These substrates bear functional groups which are not tolerated by previous methods. The organophotocatalytic process benefited from the flow parameters, affording cleaner reactions in short residence time of 13.5 mins and productivities of up to 0.65 g / day. Mechanistic studies found that catalyst derivatization not only enhanced solubility of the new catalyst compared to DCA, it profoundly diverted the photocatalytic reaction mechanism from singlet electron transfer (SET) reductive quenching with amines to energy transfer (EnT) with O2.
Enantioselective synthesis of atropisomeric indoles via iron catalysed oxidative cross-coupling
Authors: Surgenor Richard , Liu Xiangqian , Myers William , Smith Martin
Published: February 2022

Heterobiaryl compounds that exhibit axial chirality are of increasing value and interest across several fields, but direct oxidative methods for their enantioselective synthesis are elusive. Here we disclose that an iron catalyst in the presence of a chiral PyBOX ligand and an oxidant enables direct coupling between naphthols and indoles to yield atropisomeric heterobiaryl compounds with high levels of enantioselectivity. The reaction exhibits remarkable chemoselectivity and exclusively yields cross-coupled products without competing homocoupling. Mechanistic investigations enable us to postulate that an indole radical is generated in the reaction but that this is likely an off-cycle event, and that the reaction proceeds through formation of a chiral Fe-bound naphthoxy radical which is trapped by a nucleophilic indole. We envision that this simple, cheap, and sustainable catalytic manifold will facilitate access to a range of heterobiaryl compounds and enable their applications across the fields of materials science, medicinal chemistry, and catalysis.
A Data-Driven Approach to the Development and Understanding of Chiroptical Sensors for Alcohols with Remote γ-Stereocenters
Authors: Dotson Jordan , Anslyn Eric , Sigman Matthew
Published: February 2022

Dynamic covalent chemistry-based sensors have recently emerged as powerful tools to rapidly determine the enantiomeric excess of organic small molecules. While a bevy of sensors have been developed, those for flexible molecules with stereocenters remote to the functional group that binds the chiroptical sensor remain scarce. In this study, we develop an iterative, data-driven workflow to design and analyze a chiroptical sensor capable of assessing challenging acyclic γ-stereogenic alcohols. Fol-lowing sensor optimization, the mechanism of sensing was probed with a combination of computational parameterization of the sensor molecules, statistical modeling, and high-level density functional theory (DFT) calculations. These were used to elucidate the mechanism of stereochemical recognition and revealed that competing attractive non-covalent interactions (NCIs) determine the overall performance of the sensor. It is anticipated that the data-driven workflows developed herein will be generally applicable to the development and understanding of dynamic covalent and supramolecular sensors.
Alteration in H-bond strength affects the stability of codon-anticodon interaction at in-frame UAG stop codon during in vitro translation
Authors: Mala Purnima , Saraogi Ishu
Published: February 2022

We have studied the decoding ability of a non-standard nucleobase modified tRNA for non-natural amino acid mutagenesis. The insertion of 2, 6-diaminopurine (D) base at the 3rd position of a tRNA anticodon enabled us to evaluate the effect of an additional hydrogen bond during translation. The presence of D at the tRNA anticodon led to stabilization of the codon-anticodon interaction due to an additional H-bond between the N2-exocyclic amine of D and the C2 carbonyl group of uracil during protein translation. While decoding UAG codons using stop codon suppression methodology, the enhanced codon-anticodon interaction improved codon readthrough and synthesis of modified protein with a non-natural amino acid at multiple sites. Our findings imply that the number of hydrogen bonds at the tRNA-mRNA duplex interface is an important criterion during mRNA decoding and improves protein translation at multiple UAG stop sites. This work provides valuable inputs towards improved non-natural amino acid mutagenesis for creating functional proteins.
Virtual Homonuclear Decoupling in Direct Detection NMR Experiments using Deep Neural Networks
Authors: Karunanithy Gogulan , Mackenzie Harry , Hansen D Flemming
Published: February 2022

Nuclear magnetic resonance (NMR) experiments are frequently complicated by the presence of homonuclear scalar couplings. For the growing body of biomolecular 13C-detected NMR methods, one-bond 13C-13C couplings significantly reduce sensitivity and resolution. The solution to this problem has typically been to perform virtual decoupling by recording multiple spectra and taking linear combinations. Here, we propose an alternative method of virtual decoupling using deep neural networks, which only requires a single spectrum and gives a significant boost in resolution while reducing the effective phase cycles of the experiments by at least a factor of two. We successfully apply this methodology to virtually decouple in-phase CON (13CO-15N) protein NMR spectra, 13C-13C correlation spectra of protein side chains, and 13Cα-detected protein 13Cα-13CO spectra where two large homonuclear couplings are present. The deep neural network approach effectively decouples spectra with a high degree of flexibility, including in cases where existing methods fail, facilitates the use of simpler pulse sequences, and yields spectra with comparable quality to traditional virtual decoupling schemes in half the time or less.
Prebiotic synthesis of 3′-amino-TNA nucleotide triphosphates
Authors: Whitaker Daniel , Powner Matthew
Published: February 2022

Nucleic acid replication is essential to the emergence of life. Unlike canonical ribonucleotides, aminonucleotides have shown great promise in non-enzymatic replication, but are assumed to be prebiotically irrelevant due to perceived difficulties with their selective formation on the early earth. Here we demonstrate that, contrary to expectation, 3′-amino-TNA is formed diastereoselectively and regiospecifically from prebiotic feedstocks in four high-yielding steps. Our results suggest that 3′-amino-TNA may have been present on the early earth. Formation of the amino-sugar moiety by 3-component coupling of glycolaldehyde 1, 2-aminooxazole 3 and an aminonitrile 6 regiospecifically positions both the 3′-amine and glycosidic bond. Phosphate provides an unexpected resolution of the two diastereomers formed, leading to purification of the genetically relevant threo-isomer. Under phosphate catalysis, the inhibitory erythro-isomer rearranges to an unreactive guanidinium salt, whilst the Watson-Crick base paring threo-isomer co-crystalises with phosphate, leading to its spontaneous purification and accumulation. Nucleobase construction on the amino-sugar scaffold is observed upon reaction with cyanoacetylene 8, and subsequent thiolysis and photochemical anomerisation sets up the ideal stereochemistry for Watson-Crick base pairing. The resulting 3′-amino-TNA can be phosphorylated directly in water, under mild conditions with cyclic trimetaphosphate (PO3Na)3, forming a nucleotide triphosphate (NTP) in a manner not feasible for canonical nucleosides. The ease with which these activated NTPs form, and the inherent selectivity for the Watson-Crick base pairing structure, warrants further study of 3′-amino-TNA as a precursor to the genetic material of life.
Non-natural protein-protein communication mediated by a DNA-based, antibody-responsive device
Authors: Ranallo Simona , Sorrentino Daniela , Delibato Elisabetta , Ercolani Gianfranco , Plaxco Kevin W. , Ricci Francesco
Published: February 2022

We report here the rational design and optimization of an antibody responsive, DNA-based device that enables communication between pairs of otherwise non-interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the “translator,” that regulates the activity of a downstream target protein. As proof of principle, we demonstrate antibody-induced control of the proteins thrombin and Taq DNA polymerase. The resulting strategy is versatile and, in principle, can be easily adapted to control artificial protein-protein communication in artificial regulatory networks.
Catalytic Addition of Nitroalkanes to Unactivated Alkenes via Directed Carbopalladation
Authors: Simlandy Amit , Rodphon Warabhorn , Ni Hui-Qi , Gurak John , Engle Keary
Published: February 2022

We report a redox-neutral catalytic coupling of nitroalkanes and unactivated alkenes that proceeds by a directed carbopalladation mechanism. The reaction is uniquely enabled by the combination of PdI2 as the precatalyst and HFIP solvent. Structurally complex nitroalkane products, including nitro-containing carbo- and heterocycles, are prepared under operationally convenient conditions without the need for toxic or corrosive reagents. Deuterium labeling experiments and isolation of a catalytically relevant intermediate shed light on the reaction mechanism. By taking advantage of different catalytic activation modes, we demonstrate orthogonal methods for site-selective functionalization of a polyfunctional nitroalkyl ketone.
On the Role of Hydrogen Bond Strength and Charge Transfer of a Diels-Alder Reaction On-Water: Semiempirical and Free Energy Calculations.
Authors: Henao Aristizábal Andrés , Gohar Yomna , Whilhelm René , Kühne Thomas D.
Published: February 2022

Accelerated chemistry at the interface with water has received increasing attention. The mechanisms behind the enhanced reactivity On-Water are not yet clear. In this work we use a Langevin scheme in the spirit of second generation Car-Parrinello to accelerate the second-order density functional Tight-Binding (DFTB2) method in order to investigate the free energy of two Diels-Alder reaction On-Water: the cycloaddition between cyclopentadiene and ethyl cinnamate or thionocinnamate. The only difference between the reactants is the substitution of a carbonyl oxygen for a thiocarbonyl sulfur, making possible the distinction between them as strong and weak hydrogen-bond acceptors. We find a different mechanism for the reaction during the transition states and uncover the role of hydrogen bonds along with the reaction path. Our results suggest that acceleration of Diels-Alder reactions do not arise from an increased number of hydrogen bonds at the transition state and charge transfer plays a significant role. However, the presence of water and hydrogen-bonds is determinant for the catalysis of these reactions.
Reference Raman Spectrum and Mapping of Cryptosporidium parvum Oocysts
Authors: Malyshev Dmitry , Dahlberg Tobias , Öberg Rasmus , Landström Lars , Andersson Magnus
Published: February 2022

Cryptosporidium parvum is a protozoan parasite and among the most infectious diarrhea-causing pathogens, leading to severe health problems for malnourished children and immunocompromised individuals. Outbreaks are common even in developed countries, originating from water or food contamination and resulting in suffering and large costs for society. Therefore, robust, fast and highly specific detection strategies of Cryptosporidium are needed. Label-free detection techniques such as Raman spectroscopy have been suggested, however high-resolution reported spectra in the literature are limited. In this work, we report reference Raman spectra at 3 cm^{-1} resolution for viable and inactivated Cryptosporidium oocysts of the species C. parvum, gathered at a single oocyst level using a laser tweezers Raman spectroscopy system. We furthermore provide tentative Raman peak assignments for the Cryptosporidium oocysts, along with Raman mapping of the oocysts' heterogeneous internal structure. Finally, we compare the C. parvum Raman spectrum with other common enterotoxigenic pathogens: Escherichia coli, Vibrio cholerae, Bacillus cereus and Clostridium difficile. Our results show a significant difference between C. parvum Raman spectra and the other pathogens.
FOKUS BENEFAKTIF DAN INSTRUMENTAL DALAM KALIMAT IMPERATIF BAHASA JAWA
Authors: Suhandano NFN
Published: February 2022

The focus or voice system is an important issue in the study of Austronesian languages. This paper discusses the benefactive and instrumental focus in the imperative sentences of Javanese, a member of the Austronesian language with the largest number of native speakers. Through this paper, it will be shown that benefactive and instrumental in Javanese imperative sentences can be present as elements of sentences that are focused or unfocused. When they are not focused, the two elements of the sentence are expressed in prepositional phrases (PP) with the preposition of kanggo for benefactive and the preposition of nganggo for instrumental. When they are focused, the benefactive and instrumental are expressed in noun phrases (NP) and the verbs take the suffix –(k)na. Their position in the sentence structure also differs when they are focused and when they are not. The existence of imperatives with a benefactive and instrumental focus indicates that Javanese is a language of multiple voice types and this is different from the focus in declarative sentences which place Javanese into a language type with a two-voice system, active and passive. It seems that the differences focus in the two types of sentences indicates that Javanese is in the process of changing from a multiple voice type language to a two voice type language.Sistem voice atau fokus merupakan isu penting dalam studi bahasa-bahasa Austronesia. Tulisan ini membicarakan fokus benefaktif dan instrumental dalam kalimat imperatif bahasa Jawa, anggota bahasa Austronesia yang jumlah penutur aslinya paling banyak. Melalui tulisan ini akan ditunjukkan bahwa benefaktif dan instrumental dalam kalimat imperatif bahasa Jawa dapat hadir sebagai unsur kalimat yang difokuskan maupun tidak difokuskan. Ketika tidak difokuskan, kedua unsur kalimat tersebut dinyatakan dalam frasa preposisional (FP) dengan preposisi kanggo untuk benefaktif dan preposisi nganggo untuk instrumental. Ketika difokuskan, benefaktif dan instrumental diekspresikan dalam frasa nomina dan verba kalimat mengambil sufiks –(k)na. Posisinya dalam struktur kalimat juga berbeda ketika difokuskan dan tidak difokuskan. Keberadaan imperatif dengan fokus benefaktif dan instrumental mengindikasikan bahwa bahasa Jawa termasuk tipe bahasa multiple voice dan hal ini berbeda dengan fokus dalam kalimat deklaratif yang menempatkan bahasa Jawa termasuk ke dalam tipe bahasa dengan sistem dua voice, aktif dan pasif. Tampaknya perbedaan fokus dalam kedua jenis kalimat mengindikasikan bahwa bahasa Jawa sedang dalam proses perubahan dari bahasa tipe multiple voice ke bahasa tipe dua voice.
ALTERASI FITUR FONOLOGIS BAHASA BALI PASIEN AFASIA BROCA
Authors: Wardana I Ketut
Published: February 2022

The determination of phonological alteration patterns of speech disorder of Broca aphasia is the scope of neurolincguistic study that needs more attention. Thus, this study investigates the alteration of the phonological feature in Broca's aphasics. This phenomenology-based research involves the observation of two patients with nonhemorrhagic stroke with impaired language modality such as spontaneous speech, naming, reading, writing, but intact comprehension. Data was collected from observation method with listening, involvement, conversation, and noting. The data were recorded wiy Sonny voice recorder. The instruments for language modality measurements were 65 picture list, 65 word list, 1 sheet of  conversation script, and 1 reading text. The data analysis provided the implementation of generative phonology. The results showed that the substitution of marked features by less marked features due to the errors of the articulation planning program. The more complex the articulation of the phonemes, the more often the segments are altered. This study also found the violation of the sonority scale and reconstruction of the syllabic structure. The alteration of segments with the identic place of articulation with features with a different manner of articulation occurs due to phonological neighboring density. So, this study has contributed to clinical recommendations for phonological disorder for neurologists and speech therapists.Penetapan pola alterasi fonologis pada gangguan bunyi afasia Broca merupakan ruang lingkup kajian neurolinguistik yang belum begitu banyak menjadi perhatian. Penelitian ini mengkaji jenis dan pola alterasi fitur fonologis tuturan bahasa Bali pasien afasia Broca. Penelitian deskriptif berbasis fenomenologi ini melibatkan dua pasien stroke nonhemoragik (SNH) dengan pelemahan modalitas bahasa, seperti terbata-bata, penamaan, membaca, menulis, namun keupayaan pemahaman masih baik. Data dikumpulkan melalui metode pengamatan dengan teknik simak, libat, cakap, dan catat. Semua data direkam dengan Sonny voice recorder. Instrumen untuk mengukur modalitas bahasa menggunakan 65 daftar gambar, 65 daftar, kata, 1 skrip percakapan, dan 1 teks bacaan. Semua alterasi bunyi ujaran dianalisis melalui fonologi generatif. Hasil penelitian menunjukkan adanya alterasi fitur-fitur bermarkah di semua distribusi oleh fitur yang kurang bermarkah karena konsep artikulasi yang keliru. Semakin tinggi kompleksitas artikulasi bunyi, target semakin sering bunyi tersebut mengalami alterasi. Fitur bunyi dengan kompleksitas yang tinggi [+hambat] cenderung diganti dengan fitur bunyi yang kompleksitas artikulasinya setingkat lebih rendah [+frikatif]. Fonem dengan fitur fonologis bermarkah mengalami proses penyederhanaan melalui alterasi bunyi dalam bentuk substitusi, pelesapan, penyisipan, penambahan, dan mutasi. Alterasi terjadi berdasarkan kesamaan fitur tempat artikulasi, namun berbeda pada cara artikulasinya. Hasil penelitian ini dapat menjadi petunjuk ilmiah baik bagi disiplin ilmu klinisi bahasa maupun terapis gangguan berbahasa.
MODEL KEPENGAYOMAN SRI SULTAN HAMENGKU BUWONO X SAAT PANDEMI MELALUI TUTURAN “TIDHA-TIDHA” DALAM SAPA ARUH
Authors: Priambodo Marcelinus Justian
Published: February 2022

This research aims to describeconcept from 'tidha-tidha’ and analyze the affect of the concept of 'tidha-tidha' made by Sri Sultan Hamengku Buwono X  with the conceptual metaphor of the coronavirus in the society of Yogyakarta. Data in this research is internal because it is only based on the reading of Serat Kalatidha and the transcript of Sri Sultan Hamengku Buwono X's speech. This research method uses the theory ofconceptual errors in cognitive linguistic. Sri Sultan Hamengku Buwono X interprets ‘tidha-tidha’ as contemplation with ourselves, others, and God. This new disaster has made people aware of the importanceof health as a form of gratitude that must be attempted. The results reveal that perspective and frame affect the meaning of 'tidha-tidha’ made by Sri Sultan Hamengku Buwono X. The creation of this meaning has three functions consisting representative, directive, and declaration to change the conceptual metaphor of society. In his role as governor, Sri Hamengku Buwono X must change the way og communication as the leadership model and at the same time to respond that new disaster. The leadership model can be seen from the directions and instructions in the speech that are easy to understand through the intentional conceptual errors.Penelitian ini bertujuan untuk mendeskripsikan makna ‘tidha-tidha’ dan menganalisis pengaruh makna ‘tidha-tidha’ ciptaan Sri Sultan Hamengku Buwono X dengan metafora konseptual pandemi corona masyarakat DIY. Data penelitian bersifat data internal karena hanya berdasarkan pembacaan Serat Kalatidha dan hasil transkrip pidato Sri Sultan Hamengku Buwono X. Metode penelitian ini menggunakan pendekatan deskriptif analisis yang menggunakan teori erata konseptual linguistik kognitif. Hasil penelitian menunjukkan bahwa perspektif dan frame dan memengaruhi pembentukan makna ‘tidha-tidha’ ciptaan Sri Sultan Hamengku Buwono X. Sri Sultan Hamengku Buwono X memaknai ‘tidha-tidha’ sebagai kontemplasi dengan diri sendiri, sesama, dan Sang Pencipta.Bencana baru ini menyadarkan manusia pentingnya kesehatan sebagai rasa syukur yang harus diusahakan. Penciptaan makna ini memiliki tiga fungsi yaitu representatif, direktif, dan deklarasi dalam upaya mengubah metafora konseptual masyarakat. Dalam perannya sebagai gubernur, Sri Sultan Hamengku Buwono X harus mengubah cara komunikasisebagai bentuk pengayoman sekaligus menyikapi keadaan baru tersebut. Model pengayoman terlihat dari arahan dan petunjuk dalam pidato yang mudah dipahami melalui erata konseptual kesengajaan.
TINDAK PERSONA TOKOH “NDARA MAT AMIT” DAN “MBAH SIDIQ” DALAM LUKISAN KALIGRAFI KARYA A. MUSTOFA BISRI (KAJIAN PSIKOANALISIS DAN IMPLIKASINYA DALAM PENDIDIKAN MORAL ANAK)
Authors: Sidik Umar
Published: February 2022

This study aims to describe the motives of the persona of the main characters of the short stories "Ndara Mat Amit" and "Mbah Sidiq" by A. Mustofa Bisri;and what are the implications for children's moral education. The approach used in this study is the psychoanalysis of C.G. Jung, especially with regard to the act of persona. With regard to its implications in moral education, it is based on Lickona's opinion related to the importance of strategies and children's involvement in the material (reading) used. The results showed that Ndara Mat Amit acted impolite and rude persona with a motive so that his glory was not known to the public so that it could be accepted by traditional society. As a pious man who was of the Prophet Muhammad saw, he did not want to be deified, let alone cult. In addition, Ndara Mat Amit does not want to be used and co-opted by politicians who are hungry for power. Meanwhile, Mbah Sidiq acts as a pious and pious person solely to indulge worldly desires, greed. He thought that wealth would always go hand in hand with happiness and power. The implication in moral education is to discuss with children the parts where there are moral dilemmas. The teacher guides the child to be involved in the events contained in the reading. Children are asked to find answers and/or solutions to the events contained in the reading. Penelitian ini bertujuan untuk mendeskripsikan motif tindak persona tokoh utama cerpen “Ndara Mat Amit” dan “Mbah Sidiq” karya A. Mustofa Bisri; dan bagaimana implikasinya dalam pendidikan moral anak. Pendekatan yang digunakan dalam penelitian ini ialah psikoanalisis C.G. Jung, khususnya yang terkait dengan tindak persona. Berkenaan dengan implikasinya dalam pendidikan moral, digunakan pendapat Lickona yang terkait dengan pentingnya strategi dan keterlibatan anak pada materi (bacaan) yang digunakan. Hasil penelitian menunjukkan bahwa Ndara Mat Amit bertindak persona tidak santun dan kasar dengan motif agar kemuliaan dirinya tidak diketahui masyarakat sehingga dapat diterima oleh masyarakat tradisional. Sebagai seorang alim yang yang bertrah Nabi Muhammad saw., dia tidak ingin didewa-dewakan apalagi dikultuskan. Selain itu, Ndara Mat Amit tidak mau dimanfaatkan dan terkooptasi oleh politikus yang haus kekuasaan. Sementara itu, Mbah Sidiq bertindak persona alim dan linuwih semata-mata untuk memperturutkan syahwat keduniawian, nafsu keserakahan. Dia berpikir bahwa kekayaan akan selalu bersanding dengan kebahagiaan dan kekuasaan. Implikasi dalam pendidikan moralnya dapat dilakukan dengan mengajak anak mendiskusikan bagian-bagian yang memuat dilema pesan moral. Pendidik memandu agar anak terlibat ke dalam peristiwa yang terdapat dalam bacaan. Anak diminta untuk menemukan jawaban dan/atau jalan keluar atas peristiwa yang terdapat dalam bacaan.